Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_5GP-N1-BDNA-1_A23TY7KLT4_1/1241_5GP-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_5GP-N1-BDNA-1_A23TY7KLT4_1/1241_5GP-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/342193c6fdb65dad2dbc0072791592/.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/7f/342193c6fdb65dad2dbc0072791592/.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: 1241_5GP-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_5GP-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_5GP-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_5GP-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: 74985301 total, 52585 skipped (flags/unmapped)
Fragments: 37572349 total (37329493 tlen-paired, 2634 hash-paired, 391 singletons, 12842 discordant, 226989 orphans, 7699 too large [>5000 bp], 12239447 duplicates)
Reads: 80925433 total, 43362 skipped (flags/unmapped)
Fragments: 40550188 total (40305267 tlen-paired, 2330 hash-paired, 359 singletons, 9032 discordant, 233200 orphans, 7627 too large [>5000 bp], 13048326 duplicates)
Reads: 79772662 total, 47119 skipped (flags/unmapped)
Fragments: 39973991 total (39701733 tlen-paired, 4286 hash-paired, 243 singletons, 10495 discordant, 257234 orphans, 17519 too large [>5000 bp], 13167305 duplicates)
Reads: 87712707 total, 78504 skipped (flags/unmapped)
Fragments: 44024679 total (43383028 tlen-paired, 2237 hash-paired, 311 singletons, 123607 discordant, 515496 orphans, 50326 too large [>5000 bp], 14518357 duplicates)