Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_MEE-N1-BDNA-1_A23TY7KLT4_1/1241_MEE-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/e550f4101a27cb5b19565e4d258e82/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_MEE-N1-BDNA-1_A23TY7KLT4_1/1241_MEE-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  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/52/e550f4101a27cb5b19565e4d258e82/.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_MEE-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_MEE-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_MEE-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_MEE-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: 93991759 total, 65003 skipped (flags/unmapped)
Fragments: 47098288 total (46783483 tlen-paired, 4690 hash-paired, 382 singletons, 17183 discordant, 292550 orphans, 11556 too large [>5000 bp], 16624026 duplicates)
Reads: 101317383 total, 51530 skipped (flags/unmapped)
Fragments: 50770372 total (50458470 tlen-paired, 2569 hash-paired, 431 singletons, 11812 discordant, 297090 orphans, 11315 too large [>5000 bp], 17618041 duplicates)
Reads: 99974005 total, 56321 skipped (flags/unmapped)
Fragments: 50101263 total (49751590 tlen-paired, 5049 hash-paired, 390 singletons, 14924 discordant, 329310 orphans, 22429 too large [>5000 bp], 17814871 duplicates)
Reads: 109999888 total, 92369 skipped (flags/unmapped)
Fragments: 55215473 total (54403608 tlen-paired, 5238 hash-paired, 423 singletons, 154742 discordant, 651462 orphans, 64229 too large [>5000 bp], 19681057 duplicates)