Adding memory to SIngularity image

[Artifice120]

Afternoon,

I have been receiving a memory error while running juicer on a large genome (50GB) After looking through the issue posts I realized that the java memory parameter was to blame as I have 5000GB of RAM/memory available.
Unfortunately when I run the following commands:

cd /lustre/isaac/scratch/madler5/blue_pandora_seq/Genome_Assembly/juice/juiced/

export SINGULARITYENV__JAVA_OPTIONS="-Xmx500000m -Xms500000m"

export SINGULARITYENV_JAVA_OPTIONS="-Xmx500000m -Xms500000m"

_JAVA_OPTIONS="-Xmx500000m -Xms500000m" apptainer exec -B $PWD -B /lustre/isaac/scratch/madler5/blue_pandora_seq/Genome_Assembly/hifiasm/final/ \
 /lustre/isaac/scratch/madler5/blue_pandora_seq/Genome_Assembly/juice/juicer/Docker/juicer-kasm_latest.sif juicer.sh \
 -y pandora_DpnII.txt \
 -p pandora.chromer.sizes \
 -z /lustre/isaac/scratch/madler5/blue_pandora_seq/Genome_Assembly/hifiasm/final/pacbio-ont-sana-hic-1.hic.p_ctg.fa \
 -g to_juiced \
 -S final
 -T 30 -t 30

I still see the same java memory allocations in the error output.

INFO:    /etc/singularity/ exists; cleanup by system administrator is not complete (see https://apptainer.org/docs/admin/latest/singularity_migration.html)
INFO:    Environment variable SINGULARITYENV_JAVA_OPTIONS is set, but APPTAINERENV_JAVA_OPTIONS is preferred
INFO:    Environment variable SINGULARITYENV__JAVA_OPTIONS is set, but APPTAINERENV__JAVA_OPTIONS is preferred
Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m
Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m
Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m

[Artifice120]

It appears to just be a bug in the error file display. The inter.hic file shows the java memory change as it should.

HIC     pandora.chromer.sizessoftwareJuicer Tools Version 2.20.00statisticsExperiment description: Sample name HiC_sample; Juicer version 2.0; BWA 0.7.18-r1243-dirty; 48 threads; Picked up _JAVA_OPTIONS: -Xmx500000m -Xms500000m; Juicer Tools Version 2.20.00; /opt/scripts/juicer.sh -y pandora_DpnII.txt -p pandora.chromer.sizes -z /lustre/isaac/scratch/madler5/blue_pandora_seq/Genome_Assembly/hifiasm/final/pacbio-ont-sana-hic-1.hic.p_ctg.fa -g to_juiced -S final



Read type: Paired End
Sequenced Read Pairs:  271067941
No chimera found: 5918004 (2.18%)
 One or both reads unmapped: 5918004 (2.18%)
2 alignments: 205792049 (75.92%)
 2 alignments (A...B): 95471418 (35.22%)
 2 alignments (A1...A2B; A1B2...B1A2): 110320631 (40.70%)
3 or more alignments: 59357888 (21.90%)
Ligation Motif Present: N/A