DMR: processed 0 sites successfully

[Hannah1746]

I am attempting to run modkit dmr pair one some old reads and new reads.

My old_reads.bed are for a R9 cell and when I finish calling methylation I get an output file like:
Lhe_Chr1 69 70 m 3 + 69 70 255,0,0 3 0.00 0 3 0 0 0 0 0
Lhe_Chr1 70 71 m 4 - 70 71 255,0,0 4 0.00 0 4 0 1 0 0 0
Lhe_Chr1 77 78 m 1 - 77 78 255,0,0 1 100.00 1 0 0 0 0 4 0
Lhe_Chr1 99 100 m 1 - 99 100 255,0,0 1 0.00 0 1 0 0 0 4 0
Lhe_Chr1 125 126 m 2 + 125 126 255,0,0 2 0.00 0 2 0 0 0 1 1
My new_reads.bed are from R10 cell and when I finish calling methylation I get an output file like:
Lhe_Chr1 69 70 h 1 + 69 70 255,0,0 1 0.00 0 1 0 0 0 0 0
Lhe_Chr1 69 70 m 1 + 69 70 255,0,0 1 0.00 0 1 0 0 0 0 0
Lhe_Chr1 125 126 h 1 + 125 126 255,0,0 1 0.00 0 1 0 0 0 0 0
Lhe_Chr1 125 126 m 1 + 125 126 255,0,0 1 0.00 0 1 0 0 0 0 0

When I run it through 'modkit dmr pair -a old_reads.bed.gz -b new_reads.bed.gz -o ${f}DMR_RAW.bed --ref ref.fasta --base C -t 20 -f --log-filepath out.log' I am getting an output of:

reading reference FASTA at "ref.fasta"
running single-site analysis
using default prior, Beta(α: 0.55, β: 0.55)
estimating max coverages from data
sampled 364329 a records and 1920747 b records, calculating max coverages for 95th percentile
calculated max coverage for a: 22 and b: 8
finished, processed 0 sites successfully, 41178664 failed

I was hoping I could get an Idea of why nothing is passing. Is it because the old reads do not have h rows in them. Is it normal for older reads to not get h calls?

Thank you for your time!

[ArtRand]

Hello @Hannah1746,

Could you tell me if you see any messages in out.log that indicate that a scoring has failed?

[Hannah1746]

I'm sorry for wasting your time. A and B have to be the same number of individuals.

[ArtRand]

No problem. Glad you figured it out.