Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/c731c5d275f7f2eb12fa1e1a3b0c79/.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/4d/c731c5d275f7f2eb12fa1e1a3b0c79/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7Q2-N1-BDNA-1_A23NLN3LT4_1/1136_7Q2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7Q2-N1-BDNA-1_A23NLN3LT4_1/1136_7Q2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_7Q2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7Q2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_7Q2-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7Q2-N1-BDNA-1_A23NLN3LT4_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: 75014659 total, 55163 skipped (flags/unmapped)
Fragments: 37637065 total (37284638 tlen-paired, 2767 hash-paired, 341 singletons, 14010 discordant, 335309 orphans, 10508 too large [>5000 bp], 13365294 duplicates)
Reads: 81575481 total, 46604 skipped (flags/unmapped)
Fragments: 40931536 total (40562316 tlen-paired, 3104 hash-paired, 430 singletons, 9993 discordant, 355693 orphans, 10964 too large [>5000 bp], 14227227 duplicates)
Reads: 80966974 total, 48360 skipped (flags/unmapped)
Fragments: 40630111 total (40228965 tlen-paired, 6067 hash-paired, 331 singletons, 12637 discordant, 382111 orphans, 20417 too large [>5000 bp], 14537944 duplicates)
Reads: 89359753 total, 80052 skipped (flags/unmapped)
Fragments: 44979580 total (43916280 tlen-paired, 3206 hash-paired, 341 singletons, 210967 discordant, 848786 orphans, 84834 too large [>5000 bp], 16070350 duplicates)