Smoove docker cannot access files!

[Martaprf]

I am runing the docker like this:

docker run --cpus=20 --memory=25g  --memory-swap=30g \
    -v "/home/mferreira":"/input" \
    -v "/home/mferreira":"/output" \
    brentp/smoove smoove call -x \
    --name /output/all.samples.lumpy --outdir /output/teste_smoove/ \
	--fasta /input/genomeinabotle/HG002_son/SNVs_new/references_genomeinabotle/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta \
	-p 20 --genotype /input/genomeinabotle/HG002_son/alignments_joined/post_processed/*.bam

But then I get:

[smoove] 2024/09/27 08:48:30 starting with version 0.2.8
panic: open /input/genomeinabotle/HG002_son/alignments_joined/post_processed/*.bam: no such file or directory

goroutine 1 [running]:
github.com/brentp/smoove/lumpy.check(...)
        /home/brentp/src/smoove/lumpy/lumpy.go:54
github.com/brentp/smoove/lumpy.lumpy_filter_cmd(0x7fff6d91be95, 0x46, 0x7fff6d91bdf1, 0x15, 0x7fff6d91be0f, 0x74, 0x0, 0x0, 0x0, 0x0, ...)
        /home/brentp/src/smoove/lumpy/lumpy.go:83 +0xfc5
github.com/brentp/smoove/lumpy.Lumpy(0x7fff6d91bdce, 0x19, 0x7fff6d91be0f, 0x74, 0x7fff6d91bdf1, 0x15, 0xc0001fe7d0, 0x1, 0x1, 0xc0000f79a0, ...)
        /home/brentp/src/smoove/lumpy/lumpy.go:133 +0x131
github.com/brentp/smoove/lumpy.Main()
        /home/brentp/src/smoove/lumpy/lumpy.go:351 +0x29b
main.main()
        /home/brentp/src/smoove/cmd/smoove/smoove.go:121 +0x1c4

Can someone help me understand why this happen? What am I doing wrong?

Thanks

[brentp]

you could run your docker in interactive mode ("-it") to debug.
Also make sure that: /home/mferreira/genomeinabotle/HG002_son/alignments_joined/post_processed/*.bam exists on your system outside of docker.

[Martaprf]

I tried with -it and continue give the error :

docker run --cpus=20 --memory=25g  --memory-swap=30g -it \
    -v "/home/mferreira":"/input" \
    -v "/home/mferreira":"/output" \
    brentp/smoove smoove call -x \
    --name /output/all.samples.lumpy --outdir /output/teste_smoove/ \
	--fasta /input/genomeinabotle/HG002_son/SNVs_new/references_genomeinabotle/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta \
	-p 20 --genotype /input/genomeinabotle/HG002_son/alignments_joined/post_processed/*.bam

[smoove] 2024/09/27 14:17:56 starting with version 0.2.8
panic: open /input/genomeinabotle/HG002_son/alignments_joined/post_processed/*.bam: no such file or directory

goroutine 1 [running]:
github.com/brentp/smoove/lumpy.check(...)
        /home/brentp/src/smoove/lumpy/lumpy.go:54
github.com/brentp/smoove/lumpy.lumpy_filter_cmd(0x7ffff5f09e8a, 0x46, 0x7ffff5f09de6, 0x15, 0x7ffff5f09e04, 0x74, 0x0, 0x0, 0x0, 0x0, ...)
        /home/brentp/src/smoove/lumpy/lumpy.go:83 +0xfc5
github.com/brentp/smoove/lumpy.Lumpy(0x7ffff5f09dc3, 0x19, 0x7ffff5f09e04, 0x74, 0x7ffff5f09de6, 0x15, 0xc0002277e0, 0x1, 0x1, 0xc0002306e0, ...)
        /home/brentp/src/smoove/lumpy/lumpy.go:133 +0x131
github.com/brentp/smoove/lumpy.Main()
        /home/brentp/src/smoove/lumpy/lumpy.go:351 +0x29b
main.main()
        /home/brentp/src/smoove/cmd/smoove/smoove.go:121 +0x1c4

And as you can see I have one bam file in that folder :

[brentp]

maybe you need to do chmod a+r *.bam* on the files on that directory since your docker user will need access.

when you run with -it, don't send the extra arguments until you are in the shell. then in the shell you can ls and see what's actually available.

[Martaprf]

Ok, I already understand that the problem is *.bam, because if I put the all the path (/input/genomeinabotle/HG002_son/alignments_joined/post_processed//D1_S1.postprocessed.bam) it works. But how can I run for multiple files??

[brentp]

You can try escaping the * but probably the simplest way is to put the command you want to run in a shell script then:

 docker run ... bash script.sh

[Martaprf]

Thanks @brentp for all the help, I could handle with the issue, but then when the docker seemed to be running well it shows this error message:

bash: line 5:   182 Killed                  mosdepth -f /input/reference/GRCh38_full_analysis_set_plus_decoy_hla.fa --fast-mode -n --quantize 1001: /tmp/smoove-mosdepth-008384343 /output/teste_smoove//HG02568.split.bam
panic: exit status 137

goroutine 414327 [running]:
github.com/brentp/smoove/lumpy.check(...)
        /home/brentp/src/smoove/lumpy/lumpy.go:54
github.com/brentp/smoove/lumpy.remove_sketchy(0xc00013c4b0, 0x27, 0x3e8, 0x7ffc76387b82, 0x3b, 0x0, 0x0, 0xc000229500, 0x4, 0x4, ...)
        /home/brentp/src/smoove/lumpy/depthfilter.go:232 +0x1825
github.com/brentp/smoove/lumpy.remove_sketchy_all.func1(0xc000118180, 0x3e8, 0x7ffc76387b82, 0x3b, 0x0, 0x0, 0xc000229500, 0x4, 0x4, 0x1, ...)
        /home/brentp/src/smoove/lumpy/depthfilter.go:399 +0x231
created by github.com/brentp/smoove/lumpy.remove_sketchy_all
        /home/brentp/src/smoove/lumpy/depthfilter.go:397 +0x194
 

What's happen??

[brentp]

exit status 137 means not enough memory. So you'll need to tell slurm or whatever is managing your jobs to allow more memory.