Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_7QM-N1-BDNA-1_B23KGCJLT4_1/1136_7QM-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/38df940467cba00a536dd1212a122b/.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/a5/38df940467cba00a536dd1212a122b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_7QM-N1-BDNA-1_B23KGCJLT4_1/1136_7QM-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_7QM-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7QM-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai

The index file is older than the data file: 1136_7QM-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7QM-N1-BDNA-1_B23KGCJLT4_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: 77863205 total, 57339 skipped (flags/unmapped)
Fragments: 39011425 total (38751339 tlen-paired, 3662 hash-paired, 458 singletons, 17580 discordant, 238386 orphans, 10930 too large [>5000 bp], 14101868 duplicates)
Reads: 82549648 total, 46230 skipped (flags/unmapped)
Fragments: 41359328 total (41109911 tlen-paired, 2741 hash-paired, 412 singletons, 12128 discordant, 234136 orphans, 9655 too large [>5000 bp], 14727922 duplicates)
Reads: 91106250 total, 77073 skipped (flags/unmapped)
Fragments: 45705744 total (45127739 tlen-paired, 2427 hash-paired, 350 singletons, 103927 discordant, 471301 orphans, 44670 too large [>5000 bp], 16730344 duplicates)
Reads: 90798747 total, 52727 skipped (flags/unmapped)
Fragments: 45495422 total (45186186 tlen-paired, 3753 hash-paired, 322 singletons, 17611 discordant, 287550 orphans, 21524 too large [>5000 bp], 16563234 duplicates)