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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
GNU General Public License v3.0
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About memory used #49

Open yubau1112 opened 3 years ago

yubau1112 commented 3 years ago

Hi,

my paired-end fastq file: R1.fastq (250 Million reads, 150bp, ~1.2 GB) R2.fastq (250 Million reads, 150bp, ~1.2 GB)

run HLA-LA will used about 300~400 GB RAM and ~90GB swap Have any way to reduce RAM used?

my command is:

HLA-LA.pl --BAM Bwa-mem2/HLA_PM9-0232_S7.sorted.bam --graph PRG_MHC_GRCh38_withIMGT --workingDir . --sampleID HLA_LA --maxThreads 50

total time spend about 24HR~36HR

image

And another question is how can only typing some gene? because I just need class I and II gene.

thanks!

yubau

serge2016 commented 3 years ago

Any comments?

yubau1112 commented 3 years ago

@serge2016

Hi, So far, this problem has not been resolved.

AlexanderDilthey commented 11 months ago

Hi @yubau1112,

Which type of data is this? Can you try reducing the number of threads? In general, all class I and class II genes are always typed.

Best wishes

Alex