Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1047_HC-N1-BDNA-1_B23KFG5LT4_1/1047_HC-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/03d5b9f643e63fd2e4d556d8afd134/.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/d7/03d5b9f643e63fd2e4d556d8afd134/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1047_HC-N1-BDNA-1_B23KFG5LT4_1/1047_HC-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_HC-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1047_HC-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1047_HC-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_HC-N1-BDNA-1_B23KFG5LT4_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: 80142743 total, 62492 skipped (flags/unmapped)
Fragments: 40220692 total (39815428 tlen-paired, 3046 hash-paired, 436 singletons, 16955 discordant, 384827 orphans, 12065 too large [>5000 bp], 17388431 duplicates)
Reads: 84729578 total, 53037 skipped (flags/unmapped)
Fragments: 42528878 total (42111832 tlen-paired, 3307 hash-paired, 436 singletons, 11970 discordant, 401333 orphans, 10277 too large [>5000 bp], 17895828 duplicates)
Reads: 85313428 total, 55002 skipped (flags/unmapped)
Fragments: 42823180 total (42364575 tlen-paired, 3263 hash-paired, 359 singletons, 15098 discordant, 439885 orphans, 26155 too large [>5000 bp], 18503997 duplicates)
Reads: 94793188 total, 93943 skipped (flags/unmapped)
Fragments: 47731658 total (46530590 tlen-paired, 3841 hash-paired, 417 singletons, 237616 discordant, 959194 orphans, 97770 too large [>5000 bp], 20578963 duplicates)