Bug report [BUG] export_pseudobulk using new cellranger-arc v2.1 fragment files

[mariefbourdon]

Describe the bug
The export_pseudobulk function raises an error when using the outputs from new cellranger-arc 2.1. In this new version, the atac_fragments.tsv.gz file has an additional column with strand information for each fragment.

To Reproduce
Run export_pseudobulk using cellranger 2.1 fragment outputs.

Error output

2025-12-12 16:02:59,442 cisTopic     INFO     Splitting fragments by cell type.

thread '<unnamed>' panicked at src[/aggregate_fragments.rs:80:18](http://supercpu01:8624/aggregate_fragments.rs#line=79):
Invalid number of fields in fragment file!
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Expected behavior
bed and bigwig files are produced without error.

Screenshots
Example of atac_fragment.tsv.gz file in previous cellranger-arc:

Example of atac_fragment.tsv.gz file in cellranger-arc 2.1:

Version (please complete the following information):
python 3.11.8

[ghuls]

Thanks for the report. We ran into it recently ourself. Soon an update of scatac_fragment_tools will fix this.

[ghuls]

@mariefbourdon

Uninstall the current scata-fragement-tools package:

pip uninstall scatac-fragment-tools

And install the latest git version:
https://github.com/aertslab/scatac_fragment_tools?tab=readme-ov-file#from-source