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

[ghuls]

scatac_fragment_tools now has a 0.1.5 release on PyPI, so you should be able to install it with:

pip install -U scatac_fragment_tools

[nvaulin]

Hi! I got exactly the same problem and updating scatac_fragment_tools indeed resolved it. Thank you!

However, it then gives another error when i am doing export_pseudobulk (i think it is related):
TypeError: split_fragments_by_cell_barcode() missing 1 required positional argument: 'cb_prefix', it occurs here:

After some checkings I got an impression that the problem is that:

• Current rust split_fragments_by_cell_barcode function has 7 arguments, including number_of_threads in the middle and cb_prefix as the last one. (permalink), (see pic)

• It is called from the split_fragment_files_by_cell_type with 6 arguments being passed (see pic)

You can see that split_fragment_files_by_cell_type never gives it number_of_threads, so probably all the arguments go positionally, and the last one, 7th cb_prefix left empty, which explains the error message.

I can also see that in other places the number_of_threads parameter is passed explicitly. Probably copying split_fragments_by_cell_type.py line 122 to the line 87 would resolve the issue (or removing it from the rust source func). However, I don't know for sure, never used rust.

python 3.11.8
scatac_fragment_tools 0.1.5

[ghuls]

Did you restart your notebook after upgrading scatac_fragment_tools?

It seems like it is still partially using the old code as the latest version has different line numbers for the code your posted in the first screenshot than the scatac_fragments_tools 0.15 release:
https://github.com/aertslab/scatac_fragment_tools/blob/main/src/scatac_fragment_tools/library/split/split_fragments_by_cell_type.py#L79-L92

The cb_prefix part was added in the following commit.
aertslab/scatac_fragment_tools@9e2ffaf#diff-cd777203d587fe1547a810a92156650a3f7954f2ba87704b2310cfd29230d30f

The current rust code called from python calls this function (decorated with #[pyfunction]), which internally dispatches to the code you posted:
https://github.com/aertslab/scatac_fragment_tools/blob/main/rust/src/lib.rs#L39-L68