BWA-mem not working with Snakemake + singularity

Question

[brunobsouzaa]

Hi everyone, good morning. I'm falling into an issue using bwa mem inside Snakemake + Singularity, which I've investigated and can't find a way to override. BWA works fine outside singularity. The code is:

    import os                                                               
    import snakemake.io                                                     
    import glob                                                             

    configfile: "../config.yaml"                                            

    (SAMPLES,) = glob_wildcards("/home/ubuntu/samples/{sample}_R1.fastq.gz")

    # generate dag.svg diagram                                              
    # snakemake --dag all | dot -Tsvg > dag.svg                             

    rule all:                                                               
           input:
                    expand("/home/ubuntu/Germinativo/aln/inter_files/SAM/{sample}.aln.sam", sample=SAMPLES)

    rule bwa_map:
        input:
            R1="/home/ubuntu/samples/{sample}_R1.fastq.gz",
            R2="/home/ubuntu/samples/{sample}_R2.fastq.gz",
            ref=config['REF']
        output:
            sam_out="/home/ubuntu/Germinativo/aln/inter_files/SAM/{sample}.aln.sam"
        params:
            rg="@RG\\tID:lab\\tLB:AGILENT\\tSM:{sample}\\tPL:ILLUMINA"
        threads: 2
        singularity:
            "docker://biocontainers/bwa:v0.7.17_cv1"
        shell:
            "bwa mem -M -t {threads} -R '{params.rg}' {input.ref} {input.R1} {input.R2} > {output.sam_out}"

I've already followed this thread and this other thread but nothing seems to work. So, that's probably something I'm missing.

The error it shows is :

RuleException:
CalledProcessError in line 29 of /home/ubuntu/scripts/snakemake/singularity/Snakefile:
Command ' singularity exec --home /home/ubuntu/scripts/snakemake/singularity -B /home/ubuntu/samples:/data --bind /usr/lib/python3/dist-packages:/mnt/snakemake /home/ubuntu/scripts/snakem
ake/singularity/.snakemake/singularity/6443b3814f9b68bb6a33e838b8d4b84c.simg bash -c 'set -euo pipefail;  bwa mem -M -t 2 /home/ubuntu/Germinativo/GenRef/hg19/chromFa/hg19.fa /home/ubuntu
/samples/1124274_R1.fastq.gz /home/ubuntu/samples/1124274_R2.fastq.gz > /home/ubuntu/Germinativo/aln/inter_files/SAM/1124274.aln.sam'' returned non-zero exit status 1.
  File "/home/ubuntu/scripts/snakemake/singularity/Snakefile", line 29, in __rule_bwa_map
  File "/usr/lib/python3.8/concurrent/futures/thread.py", line 57, in run

Code is being run with:

snakemake -j2 --use-singularity --singularity-args "-B /home/ubuntu/samples/:/data" --verbose

Appreciate any help. Thanks in advance.

[Jeremy Leipzig]

how would Snakemake know you are now using /data instead of /home/ubuntu/samples/? and what about /home/ubuntu/Germinativo/aln/inter_files/SAM/?

[brunobsouzaa]

I'm mounting /data inside container using --singularity-args "-B /home/ubuntu/samples/:/data" The output dir is located on my local server, it should have no problem saving on it!

[Jeremy Leipzig]

normally binding syntax source_on_host:destination_in_container. so Snakemake doesn't know anything about a directory called "data" because your script hardcodes the host directories.

1. Write a hello world script that is just bash to confirm your input and output directories exist as you think
2. Write a simpler recipe in Snakemake that just moves /data/foo to /data/bar. maybe just use relative paths.
3. Build toward your bwa_map

[Jeremy Leipzig]

did you resolve this?

[brunobsouzaa]

I did not... I'm using Docker instead.