Error during execution

[frankMusacchia]

Hi,
I am having this error from lra.

Terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
myscript.sh: line 127: 1221456 Aborted (core dumped) lra align -ONT ${refHg38} ${fasta} -t 16 -
p s > ${lrasam}

do you know to what this is due?
Seems to be related to memory allocation issue. But I gave 250GB and 16 cpus to the job for its execution.

Thanks,
Francesco

[mchaisso]

Which version are you running? There was a problem pre 1.3.4 (now on conda) that ran into a bad_alloc.

[frankMusacchia]

As I need to run it within a HPC, I am running lra through a singularity container downloaded from dockerhub. Version: V1.3.2 indeed...
Additionally I have written a script that should install lra with conda in realtime. But I see same version: V1.3.2

[mchaisso]

Could it be installing from the wrong channel?
conda install -c bioconda lra

[frankMusacchia]

I have installed it with same command. And I used default channel. Do you have any different channel to use for installation?

This is the script I used:

conda update -n base -c defaults conda
conda config --add channels defaults
conda create -n singularity-env -c conda-forge singularity -y
source /bin/miniconda3/etc/profile.d/conda.sh
conda activate singularity-env

conda install --yes -c bioconda lra