catalog.alleles.tsv not looking like expected

[Kor-jent van Dijk]

Dear all,

I have been trying to run a large dataset (381 samples) through stacks.

I have run process-radtags and ustacks successfully (I think).

Followed up by cstacks on a smaller sample set to write the catalog

My species is polyploid and I am planning to feed the results into polyRAD.

I have done the full stacks run till the end with the smaller sample set, but polyRAD is not reading the catalog.alleles.tsv file.

And to be honest, it looks a bit weird. See below:

# cstacks version 2.68; catalog generated on 2025-12-10 14:02:00
1 AGG 0 0
1 AGT 0 0
1 ATG 0 0
1 ATT 0 0
1 GGT 0 0
1 GTT 0 0
2 CAGACGAANNG 0 0
2 CAGACGNACCG 0 0
2 CAGACGNACGG 0 0
2 CAGACTAANNG 0 0
2 CAGANNNANTG 0 0
2 CAGANNNATGG 0 0
2 CAGANNNNNNA 0 0
2 CAGANNNNNNG 0 0
2 CAGANNNNNNN 0 0
2 CAGANNNNNNT 0 0
2 CAGCCTAANNG 0 0
2 CAGGATAANNG 0 0
2 CAGNNGTAAAG 0 0
2 CAGNNGTAGGG 0 0
2 CAGNNNTGGAG 0 0
2 CAGTNNNNNNG 0 0
2 CGAANNNNNNN 0 0
2 CGGANNNNNNN 0 0
2 CGGNNNTGGAG 0 0
2 CGNNNNNNNCC 0 0
2 TAGACGAANNG 0 0
2 TAGACGNACGG 0 0
2 TAGANNNNNNN 0 0
3 AA 0 0
3 AN 0 0
3 AT 0 0
3 TN 0 0
3 TT 0 0
4 CATT 0 0
4 TACT 0 0
4 TATT 0 0
4 TGAA 0 0
5 AG 0 0
5 AT 0 0
5 GG 0 0
6 AAGAG 0 0
6 AAGNA 0 0
6 AAGTA 0 0
6 ACATA 0 0
6 ACGNA 0 0
6 ACGTA 0 0
6 GCGNA 0 0
6 GCGTA 0 0
7 ACCGG 0 0
7 ACGGA 0 0
7 ACGGG 0 0
7 ACGTG 0 0
7 TTGGG 0 0

I don't think I am doing anything wrong, but having all 0's is probably not ok.

Any pointers on what might be going on?

Kind regards

Kor