Empty .best and .sing2 Files After Running Demuxlet
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5 weeks ago
eking28 • 0

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

Biosciences Demuxlet • 199 views
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Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or use one of (a) the option highlighted in the image below/ (b) fenced code blocks for multi-line code. Fenced code blocks are useful in syntax highlighting. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.


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