Snakemake : CalledProcessError when running BWA on multiple files - snakemake

Question

I have a folder with multiple sub-folders that each contain .fastq files(s) that I would like to align to a genome. I am trying to create a snakemake workflow for it. First I access each sub-directory and the files in them using wildcards. Then I use the expand function to store all the paths to the files and write a rule to map the files to the genome. The code is as follows:
from snakemake.io import glob_wildcards, expand
import sys
import os
directories, files = glob_wildcards("data/samples/{dir}/{file}.fastq")
print(directories, files)
rule all:
input:
expand("data/samples/{dir}/{file}.fastq", zip, dir=directories,
file=files)
rule bwa_map:
input:
G = "data/genome.fa",
r1 = expand("data/samples/{dir}/{file}.fastq", zip,
dir=directories, file=files)
output:
r2 = expand("data/results/{dir}/{file}.bam", zip, dir=directories,
file=files)
shell:
"./bwa mem {input.G} {input.r1} | ./samtools sort -o - > {output.r2}"
However, when I execute this code as "snakemake bwa_map", I get the following error:
Error in job bwa_map while creating output files data/results/SRR5923/A.bam, data/results/SRR5924/B.bam, data/results/SRR5925/C.bam.
RuleException:
CalledProcessError in line 19 of /Users/rewatitappu/PycharmProjects/RNA-seq_Snakemake/Snakefile:
Command './bwa mem data/genome.fa data/samples/SRR5923/A.fastq data/samples/SRR5924/B.fastq data/samples/SRR5925/C.fastq | ./samtools sort -o - > data/results/SRR5923/A.bam data/results/SRR5924/B.bam data/results/SRR5925/C.bam' returned non-zero exit status 1.
File "/Users/rewatitappu/PycharmProjects/RNA-seq_Snakemake/Snakefile", line 19, in __rule_bwa_map
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/concurrent/futures/thread.py", line 55, in run
Removing output files of failed job bwa_map since they might be corrupted:
data/results/SRR5923/A.bam
Will exit after finishing currently running jobs.
Am I wrongly executing the snakemake command or could there be a problem with the code?

Answer 1

The error message suggests that the error occurred at the execution of the following shell command:
./bwa mem data/genome.fa data/samples/SRR5923/A.fastq data/samples/SRR5924/B.fastq data/samples/SRR5925/C.fastq | ./samtools sort -o - > data/results/SRR5923/A.bam data/results/SRR5924/B.bam data/results/SRR5925/C.bam
The problem could be caused by the fact that you have two bam files as output.
You probably shouldn't use expand in the bwa_map rule. The expand already took place in the all rule.