Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/03d2acf8b54c6cfe17672fe38b98e8/.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/95/03d2acf8b54c6cfe17672fe38b98e8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_8AY-N1-BDNA-1_A23NMNVLT4_1/1136_8AY-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_8AY-N1-BDNA-1_A23NMNVLT4_1/1136_8AY-N1-BDNA-1_A23NMNVLT4_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_8AY-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_8AY-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_8AY-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai

Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_8AY-N1-BDNA-1_A23NMNVLT4_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: 61265173 total, 41896 skipped (flags/unmapped)
Fragments: 30722803 total (30455814 tlen-paired, 2408 hash-paired, 219 singletons, 7796 discordant, 256566 orphans, 17228 too large [>5000 bp], 7614006 duplicates)
Reads: 57064474 total, 46679 skipped (flags/unmapped)
Fragments: 28611380 total (28383241 tlen-paired, 2476 hash-paired, 284 singletons, 8502 discordant, 216877 orphans, 6098 too large [>5000 bp], 7017304 duplicates)
Reads: 61706942 total, 41335 skipped (flags/unmapped)
Fragments: 30940507 total (30701758 tlen-paired, 2515 hash-paired, 316 singletons, 6671 discordant, 229247 orphans, 7078 too large [>5000 bp], 7400220 duplicates)
Reads: 67670517 total, 68753 skipped (flags/unmapped)
Fragments: 34020486 total (33328333 tlen-paired, 2134 hash-paired, 351 singletons, 137409 discordant, 552259 orphans, 56701 too large [>5000 bp], 8415495 duplicates)