R aborted in first command

molgenis / NIPTeR

R Package for Non Invasive Prenatal Testing (NIPT) analysis

GNU Lesser General Public License v3.0

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R aborted in first command #25

Open smruti241 opened 3 years ago

smruti241 commented 3 years ago

I am using NIPTer for the first time. When I am running this command: NIPTsample <- bin_bam_sample (bam_filepath = "my.bam" It is giving me this: Loading bam After that R aborted, new session Can you please tell me why is it happening. My bam file size is of 3.2 GB. I just dont understand.

ljohansson commented 3 years ago

Dear smruti241,

NIPTeR loads the entire bam into the memory. Because your bam file size is very large, I think the computer runs out of memory. I suggest to downsample the bam file to at least below 2 Gb. I always like using SAMtools view -s for downsampling purposes.

Cheers, Lennart

smruti241 commented 3 years ago

ok i will try. Thanks for helping me out.