Hi, i use fq2bam meth to align fastq from WGBS. but it takes too much memory. when i input a 1G file, the memory will occupy 140G. when i input a 10 G file, the program will quit suddenly after about 1 hour. The machine I am using now has an 80G GPU, 32 CPUs, and 256G RAM, and i process a 40GB file successfully in another machine. My code is:
pbrun fq2bam_meth --ref ./genome_hg38/hg38.fa --in-se-fq merge_178.fastq.gz --out-bam merge_178.bam --num-gpus 1 --bwa-nstreams 2
how to solve this problem?
the log file of this running is :
the log file of the previouse running is:
The speed of processing bases was much faster before
Hi @wangyanni541, this data public so that I can try to reproduce the issue? Thanks.
sure, thanks for the reply. This problem will be reproduced when the input data is single-cell wgbs data. It seems that the reason is that too many chains are generated. My data was downloaded from this link （GSE215353）（GEO Accession viewer. It seems that any single cell data set will encounter this problem.
1 Like
