Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/6b95d419c16948860238ab797754a1/.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/e1/6b95d419c16948860238ab797754a1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_XCZ-N1-BDNA-1_A23TY7KLT4_1/1241_XCZ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_XCZ-N1-BDNA-1_A23TY7KLT4_1/1241_XCZ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
==> 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: 1241_XCZ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_XCZ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_XCZ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_XCZ-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: 78354888 total, 56261 skipped (flags/unmapped)
Fragments: 39240318 total (39026505 tlen-paired, 3721 hash-paired, 310 singletons, 11347 discordant, 198435 orphans, 8368 too large [>5000 bp], 13240756 duplicates)
Reads: 83286930 total, 49906 skipped (flags/unmapped)
Fragments: 41714087 total (41488377 tlen-paired, 4394 hash-paired, 261 singletons, 9052 discordant, 212003 orphans, 10557 too large [>5000 bp], 14204467 duplicates)
Reads: 84647464 total, 47440 skipped (flags/unmapped)
Fragments: 42392834 total (42177344 tlen-paired, 2862 hash-paired, 359 singletons, 7648 discordant, 204621 orphans, 9668 too large [>5000 bp], 14072957 duplicates)
Reads: 91533033 total, 79640 skipped (flags/unmapped)
Fragments: 45906479 total (45348787 tlen-paired, 1467 hash-paired, 341 singletons, 106604 discordant, 449280 orphans, 45028 too large [>5000 bp], 15681721 duplicates)