Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/b325527fe0001c7dbe9b915cf754e1/.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/10/b325527fe0001c7dbe9b915cf754e1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_PRH-N1-BDNA-1_A23FG3YLT4_1/869_PRH-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_PRH-N1-BDNA-1_A23FG3YLT4_1/869_PRH-N1-BDNA-1_A23FG3YLT4_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: 869_PRH-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_PRH-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.baiThe index file is older than the data file: 869_PRH-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_PRH-N1-BDNA-1_A23FG3YLT4_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: 56226658 total, 40969 skipped (flags/unmapped)
Fragments: 28210758 total (27955063 tlen-paired, 3311 hash-paired, 326 singletons, 7707 discordant, 244351 orphans, 4425 too large [>5000 bp], 7012393 duplicates)
Reads: 61898098 total, 40440 skipped (flags/unmapped)
Fragments: 31055317 total (30761011 tlen-paired, 4274 hash-paired, 307 singletons, 7736 discordant, 281989 orphans, 14660 too large [>5000 bp], 7627604 duplicates)
Reads: 61629098 total, 37131 skipped (flags/unmapped)
Fragments: 30924197 total (30643540 tlen-paired, 2491 hash-paired, 392 singletons, 5651 discordant, 272123 orphans, 8044 too large [>5000 bp], 7535409 duplicates)
Reads: 63033568 total, 68749 skipped (flags/unmapped)
Fragments: 31748760 total (30927314 tlen-paired, 3036 hash-paired, 384 singletons, 157527 discordant, 660499 orphans, 64091 too large [>5000 bp], 7763230 duplicates)