Error with running cellranger-atac count

Question

[Khôi]

Hi everyone, I was running cellranger-atac count on a mouse brain sample when I encountered the following errors:

Traceback (most recent call last):
  File "/software/cellranger-atac-1.2.0/martian-cs/v3.2.4/adapters/python/martian_shell.py", line 589, in _main
    stage.main()
  File "/software/cellranger-atac-1.2.0/martian-cs/v3.2.4/adapters/python/martian_shell.py", line 560, in main
    self._run(lambda: self._module.join(
  File "/software/cellranger-atac-1.2.0/martian-cs/v3.2.4/adapters/python/martian_shell.py", line 523, in _run
    cmd()
  File "/software/cellranger-atac-1.2.0/martian-cs/v3.2.4/adapters/python/martian_shell.py", line 561, in <lambda>
    args, outs, chunk_defs, chunk_outs))
  File "/software/cellranger-atac-1.2.0/cellranger-atac-cs/1.2.0/mro/atac/stages/processing/cell_calling/detect_cell_barcodes/__init__.py", line 421, in join
    summary_info.update(generate_gb_metrics(cell_barcodes, excluded_barcodes))
  File "/software/cellranger-atac-1.2.0/cellranger-atac-cs/1.2.0/mro/atac/stages/processing/cell_calling/detect_cell_barcodes/__init__.py", line 456, in generate_gb_metrics
    "fraction_gelbead_doublets_cells": 1 - (estimated_doublet_noncell_gelbeads / estimated_doublet_gelbeads),
ZeroDivisionError: division by zero`

Here's the code I ran:

    cellranger-atac count \\
    --id $meta \\
    --reference $ref_atac_genome \\
    --fastqs fastq_files/ \\
    --sample $meta \\
    --localcores $task.cpus

reference was: refdata-cellranger-atac-mm10-1.2.0 and the fastq files are respectively R1, R2, R3

It seems that the tool detects 0 doublet gelbeads, I was wondering whether this could mean anything? Before processing the fastq files with the count command, I was trimming primer & linker sequences according to a paper I was looking at. Could anyone point me towards at potential causes? Thank you.

[GenoMax]

Before processing the fastq files with the count command, I was trimming primer & linker sequences according to a paper I was looking at.

Have you tried to run the counts with original files? Not clear what you did in the process, but you may have borked the data in some way.