Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_2RO-N1-BDNA-1_A237CFYLT3_1/1136_2RO-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_2RO-N1-BDNA-1_A237CFYLT3_1/1136_2RO-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/d0c0a63422f0ae83483ec9c9c4637a/.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/23/d0c0a63422f0ae83483ec9c9c4637a/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_2RO-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 1136_2RO-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_2RO-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2RO-N1-BDNA-1_A237CFYLT3_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: 83248823 total, 90190 skipped (flags/unmapped)
Fragments: 41946884 total (41167811 tlen-paired, 7844 hash-paired, 14028 singletons, 10800 discordant, 746401 orphans, 12647 too large [>5000 bp], 9630456 duplicates)
Reads: 82344201 total, 96057 skipped (flags/unmapped)
Fragments: 41484834 total (40731098 tlen-paired, 6260 hash-paired, 14449 singletons, 12114 discordant, 720913 orphans, 6919 too large [>5000 bp], 9590634 duplicates)
Reads: 91207322 total, 90921 skipped (flags/unmapped)
Fragments: 45960267 total (45116496 tlen-paired, 6443 hash-paired, 15085 singletons, 9531 discordant, 812712 orphans, 11832 too large [>5000 bp], 10523445 duplicates)
Reads: 95522370 total, 207248 skipped (flags/unmapped)
Fragments: 48505536 total (45847730 tlen-paired, 6955 hash-paired, 15969 singletons, 535945 discordant, 2098937 orphans, 209478 too large [>5000 bp], 10928480 duplicates)