Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_JOS-N1-BDNA-1_A23TY7KLT4_1/1241_JOS-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/22c6e3b8cc6a6948472c8f86a06e69/.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/9d/22c6e3b8cc6a6948472c8f86a06e69/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_JOS-N1-BDNA-1_A23TY7KLT4_1/1241_JOS-N1-BDNA-1_A23TY7KLT4_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: 1241_JOS-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_JOS-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_JOS-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_JOS-N1-BDNA-1_A23TY7KLT4_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: 71744798 total, 54692 skipped (flags/unmapped)
Fragments: 35923758 total (35734407 tlen-paired, 4344 hash-paired, 255 singletons, 10005 discordant, 174747 orphans, 8796 too large [>5000 bp], 12257714 duplicates)
Reads: 77208829 total, 42710 skipped (flags/unmapped)
Fragments: 38665958 total (38476143 tlen-paired, 3322 hash-paired, 307 singletons, 7300 discordant, 178886 orphans, 6698 too large [>5000 bp], 13003582 duplicates)
Reads: 76390227 total, 46067 skipped (flags/unmapped)
Fragments: 38256431 total (38049157 tlen-paired, 3995 hash-paired, 242 singletons, 8871 discordant, 194166 orphans, 12853 too large [>5000 bp], 13191643 duplicates)
Reads: 83992054 total, 75265 skipped (flags/unmapped)
Fragments: 42113370 total (41628122 tlen-paired, 3058 hash-paired, 260 singletons, 93155 discordant, 388775 orphans, 39542 too large [>5000 bp], 14554753 duplicates)