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 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...