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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.
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.
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.
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.
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