Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BSWE-N1-BDNA-1_235YY7LT3_1/1029_BSWE-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/e483b2fbb254c5e9a37c55b93a7403/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/e483b2fbb254c5e9a37c55b93a7403/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BSWE-N1-BDNA-1_235YY7LT3_1/1029_BSWE-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BSWE-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BSWE-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BSWE-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BSWE-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 69730069 total, 58342 skipped (flags/unmapped)
Fragments: 35002090 total (34646512 tlen-paired, 3133 hash-paired, 4447 singletons, 11146 discordant, 336852 orphans, 4423 too large [>5000 bp], 8567579 duplicates)
Reads: 77584449 total, 87820 skipped (flags/unmapped)
Fragments: 39110892 total (37995654 tlen-paired, 4500 hash-paired, 4713 singletons, 211021 discordant, 895004 orphans, 87281 too large [>5000 bp], 9467541 duplicates)
Reads: 75201185 total, 54542 skipped (flags/unmapped)
Fragments: 37746820 total (37369855 tlen-paired, 3709 hash-paired, 4553 singletons, 8117 discordant, 360586 orphans, 9071 too large [>5000 bp], 9113202 duplicates)
Reads: 76725654 total, 57704 skipped (flags/unmapped)
Fragments: 38510973 total (38109789 tlen-paired, 4640 hash-paired, 4764 singletons, 10882 discordant, 380898 orphans, 15833 too large [>5000 bp], 9354546 duplicates)