Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/61/6e1a8b4a91bf3a9e54413e8d30dfc6/.command.sh
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/93/9708b3ec418f8f5b29b8b5d30e4ab1/four.markdup.bam.bai
  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/61/6e1a8b4a91bf3a9e54413e8d30dfc6/.command.run
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/93/9708b3ec418f8f5b29b8b5d30e4ab1/four.markdup.bam
==> STAGING COMPLETE (5 inputs)

/usr/local/lib64/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: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: four.markdup.bam.bai
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