Memory exhaustion using microphaser somatic

[omidalam]

Hello all,

I'm trying to phase tumor DNA sequences using microphaser. I want to optimize for MHCII binding, and therefore I'm using window_length of 45.
I run one script for each of the chromosomes, which I have created a separated GTF file for each chromosome.

microphaser somatic results/recal/A_tumor.sorted.bam --variants results/strelka/merged/A_tumor/all_variants.norm.annotated.bcf 
--ref resources/genome.fasta 
--tsv results/microphaser/info/A_tumor/A_tumor.6.tsv 
-n results/microphaser/fasta/A_tumor/A_tumor.6.wt.fa 
-w 45 < resources/annotation/6.gtf > results/microphaser/fasta/A_tumor/A_tumor.6.mt.fa

It runs ok for all the chromosomes, but for chromosome 6 it starts using up the RAM and subsequently killed (the machine has 32GB RAM + 32GB swap). I am using Ubuntu 22.04.1 LTS and I run the script inside a conda environment. I have tried different microphaser versions and all end up with the same issue. Below is the conda list output for microphaser 0.7.0.

I tried using a smaller window_length, and it works fine with 27.

Any idea what's going wrong?

Best,
Omid.

# packages in environment at /root/miniconda3/envs/microphaser0.7:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
blis                      0.9.0                h166bdaf_0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
microphaser               0.7.0                h33b3098_1    bioconda
openssl                   1.1.1s               h0b41bf4_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge