Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_0UA-N1-BDNA-1_A23H3W5LT3_1/1136_0UA-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_0UA-N1-BDNA-1_A23H3W5LT3_1/1136_0UA-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/5450177f374d57b1cdd2c8d9244e70/.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/d9/5450177f374d57b1cdd2c8d9244e70/.command.run
==> 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: 1136_0UA-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0UA-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0UA-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0UA-N1-BDNA-1_A23H3W5LT3_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: 40717475 total, 38861 skipped (flags/unmapped)
Fragments: 20492072 total (20163914 tlen-paired, 3172 hash-paired, 2700 singletons, 4728 discordant, 317558 orphans, 7364 too large [>5000 bp], 3791856 duplicates)
Reads: 40975075 total, 32560 skipped (flags/unmapped)
Fragments: 20632085 total (20290720 tlen-paired, 3988 hash-paired, 2562 singletons, 3946 discordant, 330869 orphans, 5888 too large [>5000 bp], 3794114 duplicates)
Reads: 44594792 total, 32024 skipped (flags/unmapped)
Fragments: 22459347 total (22086967 tlen-paired, 3027 hash-paired, 2830 singletons, 3523 discordant, 363000 orphans, 4952 too large [>5000 bp], 4121941 duplicates)
Reads: 46378928 total, 55811 skipped (flags/unmapped)
Fragments: 23542415 total (22352757 tlen-paired, 3266 hash-paired, 2968 singletons, 240915 discordant, 942509 orphans, 91882 too large [>5000 bp], 4250200 duplicates)