singularity - Error in value

[cathalgking]

I successfully pulled the numbat container with singularity instead of Docker (our HPC only has singularity) with the following:

singularity pull docker://pkharchenkolab/numbat-rbase:main

That created a .sif file which contains all the neccessary files such as Eagle_v2.4.1, 1000G_hg38.zip etc.

When I try to run the pre-processing script (pileup_and_phase.R) I am met with an Error

Error in value[[3L]](cond) : Pileup failed
Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

I am running this with

singularity exec numbat-rbase_main.sif Rscript /numbat/inst/bin/pileup_and_phase.R \
...

The output to the screen starts with:

Using genome version: hg38
Running pileup
[I::main] start time: 2024-02-01 10:57:51
[W::check_args] Max depth set to maximum value (2147483647)
[W::check_args] Max pileup set to maximum value (2147483647)
[I::main] global settings after checking:
	num of input files = 1
...

What could be causing this issue?
Thanks

[teng-gao]

Hi, we haven't tested the container with singularity .. maybe attach the full output message on the screen?

[cathalgking]

@teng-gao
I believe singularity can operate on a Docker image in the same way. When I run some initial checks on the container it seems to contain all the necessary packages and data. The full output to the screen is shown below, when I try to prepare the allele data by running the pileup_and_phase.R numbat script.

[cathalgking]

Hi @teng-gao, just following up on this. Have you had any chance to take a look at this error? Thanks

[teng-gao]

Looks like the container doesn't have access to the SNP file.