vireo detects 0 variants

[DanielMedinaCano]

Hi,

First of all, thank you so much for developing cellsnp-lite and vireo, it has saved our lab a lot of money.
I'm used to run them on scRNA-seq data but now I'm trying to run it for the first time on scATAC-seq data. cellsnp-lite seems to work properly (with --UMItag None), but then vireo detects 0 variants within the cellsnp-lite output files. I've manually inspected the cellSNP.base.vcf file and I can't see any difference comapred to the files that I obtain from scRNA-seq. Do you know what could be causing this?

I run:
cellsnp-lite -s /data/.../possorted_bam.bam -b /data/.../barcodes.tsv -O /data/.../demulti -R /data/.../Four_F1s.vcf.gz -p 20 --minMAF 0.1 --minCOUNT 20 --UMItag None –gzip
and then
vireo -c /data/.../demulti -N 4 -o /data/.../demulti

Here's the output from cellsnp-lite:
[I::main] start time: 2022-08-10 11:01:30
[I::main] loading the VCF file for given SNPs ...
[I::main] fetching 68533341 candidate variants ...
[I::main] mode 1a: fetch given SNPs in 5392 single cells.
[I::csp_fetch_core][Thread-7] 2.00% SNPs processed.
.....
[I::csp_fetch_core][Thread-12] 98.00% SNPs processed.
[I::main] All Done!
[I::main] end time: 2022-08-10 14:18:51
[I::main] time spent: 11841 seconds.

And the vireo one:
[vireo] Loading cell folder ...
[vireo] Demultiplex 5392 cells to 4 donors with 0 variants.
Traceback (most recent call last):
File "/opt/anaconda3/bin/vireo", line 8, in
sys.exit(main())
File "/opt/anaconda3/lib/python3.9/site-packages/vireoSNP/vireo.py", line 204, in main
res_vireo = vireo_wrap(cell_dat['AD'], cell_dat['DP'], n_donor=n_donor,
File "/opt/anaconda3/lib/python3.9/site-packages/vireoSNP/utils/vireo_wrap.py", line 86, in vireo_wrap
_models_all[im].fit(AD, DP, min_iter=5, max_iter=max_iter_init,
File "/opt/anaconda3/lib/python3.9/site-packages/vireoSNP/utils/vireo_model.py", line 307, in fit
ELBO = self._fit_VB(AD, DP, max_iter, min_iter, epsilon_conv,
File "/opt/anaconda3/lib/python3.9/site-packages/vireoSNP/utils/vireo_model.py", line 261, in _fit_VB
self.update_GT_prob(AD, DP)
File "/opt/anaconda3/lib/python3.9/site-packages/vireoSNP/utils/vireo_model.py", line 209, in update_GT_prob
S2_gt = SS_gt - S1_gt
ValueError: operands could not be broadcast together with shapes (684269,4) (0,4)

Thanks in advance and have a great day,
Dani