I am running this command through the Demuxlet authors' docker container, yimmieg/demuxlet:
docker run \
-v $(pwd):/data \
--user $(id -u):$(id -g) \
yimmieg/demuxlet \
--sam /data/sorted_some_ipsc.bam \
--tag-group CB \
--tag-UMI pN \
--vcf /data/small_really_reorganized.vcf \
--field GT \
--out /data/small_CB_pN \
--sam-verbose 10000000 \
--vcf-verbose 100000
(The .bam file comes from scRNA-seq data using a Parse Biosciences kit, hence the pN UMI tag.)
When I run this command, I get a .single file and empty .best and .sing2 files. I also get this message:
terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc
I have read that this is a memory issue. But these .bam and .vcf files are subsets of small datasets, 800 and 200 MB respectively. And this is being run on a fairly powerful virtual machine.
What is going wrong? Any help would be appreciated
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