Error: object 'barcodes' not found in bulk mode

[ctho1]

Hello,

I am using the latest numbat Docker container and attempting to analyze bulk RNA-seq data with the following command:

Rscript /numbat/inst/bin/pileup_and_phase.R \
  --label sample \
  --samples sample \
  --bams /mnt/mydata/sample.bam \
  --outdir /mnt/mydata/sample \
  --gmap /Eagle_v2.4.1/tables/genetic_map_hg38_withX.txt.gz \
  --snpvcf /data/genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf \
  --paneldir /data/1000G_hg38 \
  --ncores 10 \
  --bulk

However, this results in the following error:

Running in Bulk mode
Using genome version: hg38
Error: object 'barcodes' not found
Execution halted

It seems that the script is still expecting a barcodes object, even though bulk mode should not require it.
I also tried passing a dummy --barcodes argument, but the error persists.

Could you clarify whether this is a bug or if there’s an additional argument needed to run bulk mode properly?

Thank you for your help!

Christian

[Thapeachydude]

I'm running into the same problem. Where you able to solve it?

Edit: it seems that creating and specifying a dummy .txt file will do the trick.