LJA container fails: "Child process crashed"

[MrTomRod]

I failed to run lja using the containers quay.io/biocontainers/lja:0.2--h5b5514e_2 and quay.io/biocontainers/lja:0.2--h5b5514e_1. I think they were made by @zilov in issue #39730.

First, it seems to run fine, but then it crashes with:

...
00:00:49 58Mb  INFO: Increasing k
00:00:49 58Mb  INFO: Finished increasing k
00:00:49 58Mb  INFO: Exporting remaining active transitions
00:00:49 58Mb  INFO: Export to Dot
00:00:49 58Mb  INFO: Export to GFA and compressed contigs
00:00:49 78Mb  INFO: Finished repeat resolution
00:00:49 4Mb  INFO: Performing polishing and homopolymer uncompression
00:00:50 14Mb  INFO: Aligning reads back to assembly
00:00:51 249Mb  INFO: Finished alignment.
00:00:51 249Mb  INFO: Printing alignments to "out_2/uncompressing/alignments.txt"
00:00:51 309Mb  INFO: Reading and processing initial reads from ["reads.fastq.gz"]
00:01:03 0.6Gb  INFO: Uncompressing homopolymers in contigs
Child process crashed

Tested on my laptop (apptainer and podman) as well as our HPC (apptainer). It works with my own container (troder/lja) using identical input data. Below my Dockerfile, in case that helps. See also AntonBankevich/LJA#37.

FROM debian:bullseye
MAINTAINER Thomas Roder

RUN apt update
RUN apt install -y build-essential cmake zlib1g-dev wget

WORKDIR /opt
RUN wget https://github.com/AntonBankevich/LJA/archive/refs/tags/untagged-c539e6b1159980742576.tar.gz -O LJA.tar.gz && \
mkdir LJA && tar -xf LJA.tar.gz --strip-components=1 -C LJA && rm LJA.tar.gz

WORKDIR /opt/LJA
RUN cmake . && make

ENV PATH="/opt/LJA/bin:${PATH}"

WORKDIR /data