Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/e39231de7dc0e766b418d679657718/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_32X-N1-BDNA-1_B23KGCJLT4_1/1136_32X-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_32X-N1-BDNA-1_B23KGCJLT4_1/1136_32X-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  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/fe/e39231de7dc0e766b418d679657718/.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_32X-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_32X-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_32X-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_32X-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: 64597830 total, 35419 skipped (flags/unmapped)
Fragments: 32376877 total (32160406 tlen-paired, 1477 hash-paired, 304 singletons, 8011 discordant, 206679 orphans, 7820 too large [>5000 bp], 11884501 duplicates)
Reads: 60587593 total, 46006 skipped (flags/unmapped)
Fragments: 30366684 total (30144939 tlen-paired, 3004 hash-paired, 362 singletons, 11992 discordant, 206387 orphans, 7484 too large [>5000 bp], 11400276 duplicates)
Reads: 71750283 total, 61012 skipped (flags/unmapped)
Fragments: 36031478 total (35457111 tlen-paired, 1899 hash-paired, 341 singletons, 108111 discordant, 464016 orphans, 45336 too large [>5000 bp], 13596325 duplicates)
Reads: 71503287 total, 39883 skipped (flags/unmapped)
Fragments: 35840092 total (35569043 tlen-paired, 3729 hash-paired, 286 singletons, 12598 discordant, 254436 orphans, 18971 too large [>5000 bp], 13503389 duplicates)