Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/60/76a51779eb87e7051cb2eff752360b/one.markdup.bam.bai
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/2f/6591d360df6c3d77bf2fe1170559ab/.command.sh
  Downloading: s3://fsdx-algo-644019535899-us-west-2-an/aschultz/bf-gui-test/small_padded.bed
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/60/76a51779eb87e7051cb2eff752360b/one.markdup.bam
  Downloading: s3://fsdx-algo-644019535899-us-west-2-an/aschultz/bf-gui-test/small.bed
  Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.fai
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/2f/6591d360df6c3d77bf2fe1170559ab/.command.run
==> STAGING COMPLETE (8 inputs)

/usr/local/lib/python3.11/site-packages/numpy/_core/fromnumeric.py:54: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead.
  return bound(*args, **kwds)
[W::hts_idx_load3] The index file is older than the data file: one.markdup.bam.bai
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: one.markdup.bam.bai
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: one.markdup.bam.bai
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: one.markdup.bam.bai
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: one.markdup.bam.bai
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: one.markdup.bam.bai
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: one.markdup.bam.bai
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: one.markdup.bam.bai
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: one.markdup.bam.bai
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
[W::hts_idx_load3] The index file is older than the data file: one.markdup.bam.bai
[mpileup] 1 samples in 1 input files
[mpileup] Combined max depth is above 1M. Potential memory hog!
Done. Merging outputs