Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/7ac3f913bcc8fc210383916f3de875/.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/51/7ac3f913bcc8fc210383916f3de875/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_cVw-N1-BDNA-1_B23KGCJLT4_1/659_cVw-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/659_cVw-N1-BDNA-1_B23KGCJLT4_1/659_cVw-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] The index file is older than the data file: 659_cVw-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cVw-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cVw-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cVw-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: 87211015 total, 63315 skipped (flags/unmapped)
Fragments: 43698083 total (43408883 tlen-paired, 3507 hash-paired, 546 singletons, 17403 discordant, 267744 orphans, 9912 too large [>5000 bp], 17802475 duplicates)
Reads: 93581763 total, 58533 skipped (flags/unmapped)
Fragments: 46893323 total (46576998 tlen-paired, 3771 hash-paired, 380 singletons, 14250 discordant, 297924 orphans, 17444 too large [>5000 bp], 19232442 duplicates)
Reads: 93600214 total, 54775 skipped (flags/unmapped)
Fragments: 46896231 total (46609529 tlen-paired, 3648 hash-paired, 558 singletons, 12191 discordant, 270305 orphans, 11920 too large [>5000 bp], 18724145 duplicates)
Reads: 102920055 total, 89944 skipped (flags/unmapped)
Fragments: 51643768 total (50931386 tlen-paired, 4024 hash-paired, 426 singletons, 134571 discordant, 573361 orphans, 58181 too large [>5000 bp], 21251388 duplicates)