hmmratac: ValueError: Adjust --means and --stddev options and re-run command

[bbimber]

Describe the bug

I am running hmmratac on bulk ATAC-seq data. I am following the tutorial on your documentation site. The command reads all the BAM reads, but then dies with the error "ValueError: Adjust --means and --stddev options and re-run command". I believe I am running this specifically to determine those parameters, and dont see much in your docs on these (https://macs3-project.github.io/MACS/docs/hmmratac.html). Is this error something you've seen before, and do you have any debugging suggestions?

My command is:

macs3 hmmratac -i fred.p0.bam -f BAMPE --cutoff-analysis-only -n Fred_P0

and here is the output:

INFO  @ 07 Apr 2025 05:49:51: [129 MB] 
# Command line: hmmratac -i fred.p0.bam -f BAMPE --cutoff-analysis-only -n Fred_P0
# Random seed selected as: 10151
# Use --hmm-type to select a Gaussian ('gaussian') or Poisson ('poisson') model for the hidden markov model in HMMRATAC. Default: 'gaussian'. 
 
INFO  @ 07 Apr 2025 05:49:51: [129 MB] #1 Read fragments from BAMPE file... 
INFO  @ 07 Apr 2025 05:49:53: [156 MB]  1000000 fragments parsed 
<Skipping middle....>
INFO  @ 07 Apr 2025 06:05:46: [5225 MB]  393000000 fragments parsed 
INFO  @ 07 Apr 2025 06:05:49: [5232 MB] 393919456 fragments have been read. 
INFO  @ 07 Apr 2025 06:09:38: [5232 MB] #  Read 393919456 fragments. 
INFO  @ 07 Apr 2025 06:09:38: [5232 MB] #2 Use EM algorithm to estimate means and stddevs of fragment lengths 
INFO  @ 07 Apr 2025 06:09:38: [5232 MB] #  for mono-, di-, and tri-nucleosomal signals... 
INFO  @ 07 Apr 2025 06:09:38: [5232 MB] # A random seed 10151 has been used in the sampling function 
INFO  @ 07 Apr 2025 06:11:36: [5841 MB] # Downsampled 12757238 fragments will be used for EM training... 
 ValueError:  Adjust --means and --stddev options and re-run command

System (please complete the following information):

• OS: Linux
• Python version: 3.13
• MACS Version 3.0.3