Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_e9a-N1-BDNA-1_A23TNVNLT4_1/659_e9a-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/fd55c1b4e449692cd9f8ffc4770a5b/.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/20/fd55c1b4e449692cd9f8ffc4770a5b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_e9a-N1-BDNA-1_A23TNVNLT4_1/659_e9a-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
==> 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: 659_e9a-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_e9a-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_e9a-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 659_e9a-N1-BDNA-1_A23TNVNLT4_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: 115824755 total, 81288 skipped (flags/unmapped)
Fragments: 58059677 total (57630103 tlen-paired, 5791 hash-paired, 512 singletons, 21998 discordant, 401273 orphans, 12949 too large [>5000 bp], 22018500 duplicates)
Reads: 124772448 total, 70510 skipped (flags/unmapped)
Fragments: 62551115 total (62073260 tlen-paired, 5637 hash-paired, 435 singletons, 19710 discordant, 452073 orphans, 26108 too large [>5000 bp], 24070843 duplicates)
Reads: 125594509 total, 68481 skipped (flags/unmapped)
Fragments: 62959947 total (62522599 tlen-paired, 4224 hash-paired, 546 singletons, 16134 discordant, 416444 orphans, 11562 too large [>5000 bp], 23521445 duplicates)
Reads: 138040629 total, 132798 skipped (flags/unmapped)
Fragments: 69328096 total (68166961 tlen-paired, 6421 hash-paired, 531 singletons, 225757 discordant, 928426 orphans, 90298 too large [>5000 bp], 26704782 duplicates)