Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/29/8c5f41ece550ff51a3ce65080275fd/two.markdup.bam.bai
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/29/8c5f41ece550ff51a3ce65080275fd/two.markdup.bam
  Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/dc/1f059f2aacb5076aad925d1648e2b5/.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/dc/1f059f2aacb5076aad925d1648e2b5/.command.run
==> 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: two.markdup.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.baiThe index file is older than the data file: two.markdup.bam.bai

The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
[W::hts_idx_load3] The index file is older than the data file: two.markdup.bam.bai
Chunk 6 processed...
Chunk 7 processed...
Chunk 8 processed...
Chunk 9 processed...
Chunk 10 processed...
Chunk 11 processed...
Chunk 14 processed...
Chunk 15 processed...
Chunk 26 processed...
Chunk 27 processed...
Chunk 28 processed...
Chunk 29 processed...
Chunk 4 processed...
Chunk 5 processed...
Chunk 12 processed...
Chunk 13 processed...
Chunk 0 processed...
Chunk 1 processed...
Chunk 22 processed...
Chunk 23 processed...
Chunk 24 processed...
Chunk 25 processed...
Chunk 2 processed...
Chunk 3 processed...
Chunk 16 processed...
Chunk 17 processed...
Chunk 18 processed...
Chunk 19 processed...
Chunk 20 processed...
Chunk 21 processed...