Output yml didn't show bias information after specifying bias_specs for training model

[Yanbo-Xu]

Hi, I used bpnet train ${yml} ${outdir} --premade=bpnet9 --config=/home/xuyanbo/software/bpnet/examples/zebrafish_chip_seq/config.gin --in-memory --num-workers=24 This command trains the model. In the yml specified by the training command, I set the bias_specs. but in the output yml, I don't seem to find any information about the corresponding bias_specs, why is that?

Here is the yml of the model:

fasta_file: /home/xuyanbo/raw_data/bam20241230/danRer11.fa
task_specs.
  zebrafish.
    tracks. 
      - /home/xuyanbo/bpnet/input/bcchip.pos.bw
      - /home/xuyanbo/bpnet/input/bcchip.neg.bw
    peaks: /home/xuyanbo/bpnet/output/02peaks/peaks_test.bed

bias_specs.
  /home/bpnet/output/02peaks/peaks_test.bed
    tracks. 
      - /home/xuyanbo/bpnet/input/bcinput.pos.bw
      - /home/xuyanbo/bpnet/input/bcinput.neg.bw
    tasks: zebrafish 
      - zebrafish

This is the yml in the output directory:

task_specs.
  zebrafish.
    tracks.
    - /home/xuyanbo/bpnet/input/bcchip.pos.bw
    - /home/xuyanbo/bpnet/input/bcchip.neg.bw
    peaks: /home/xuyanbo/bpnet/output/02peaks/peaks_test.bed
    sum_tracks: false
fasta_file: /home/xuyanbo/raw_data/bam20241230/danRer11.fa
bias_specs: {}
path: /home/xuyanbo/software/bpnet/examples/zebrafish_chip_seq/dataspec.yml

[Yanbo-Xu]

I tried using the same input, but without specifying bias_specs in dataspec.yml. After comparing the two times, the results are significantly different, suggesting that the bias_specs actually played a role before, they just didn't show up in the output.