Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_2QY-N1-BDNA-1_A237CFYLT3_1/1136_2QY-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/70a45730b9cca4a67af2d287a679b9/.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/88/70a45730b9cca4a67af2d287a679b9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_2QY-N1-BDNA-1_A237CFYLT3_1/1136_2QY-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
==> 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_2QY-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QY-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QY-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QY-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: 58684493 total, 57089 skipped (flags/unmapped)
Fragments: 29619943 total (28970408 tlen-paired, 3229 hash-paired, 7814 singletons, 6810 discordant, 631682 orphans, 13507 too large [>5000 bp], 5152009 duplicates)
Reads: 58098555 total, 62563 skipped (flags/unmapped)
Fragments: 29319418 total (28697332 tlen-paired, 3926 hash-paired, 7901 singletons, 7566 discordant, 602693 orphans, 3875 too large [>5000 bp], 5120292 duplicates)
Reads: 64252207 total, 59377 skipped (flags/unmapped)
Fragments: 32438812 total (31730729 tlen-paired, 3647 hash-paired, 8633 singletons, 5990 discordant, 689813 orphans, 6826 too large [>5000 bp], 5636340 duplicates)
Reads: 67269566 total, 139360 skipped (flags/unmapped)
Fragments: 34293764 total (32021575 tlen-paired, 3066 hash-paired, 8851 singletons, 458165 discordant, 1802107 orphans, 176818 too large [>5000 bp], 5845055 duplicates)