Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_67V-N1-BDNA-1_A23MHW3LT4_1/1136_67V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/de3ccde1f689cb0013507cac08eadd/.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/00/de3ccde1f689cb0013507cac08eadd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_67V-N1-BDNA-1_A23MHW3LT4_1/1136_67V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_67V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_67V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_67V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_67V-N1-BDNA-1_A23MHW3LT4_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: 53458048 total, 42396 skipped (flags/unmapped)
Fragments: 26960527 total (26430025 tlen-paired, 2317 hash-paired, 284 singletons, 6073 discordant, 521828 orphans, 8355 too large [>5000 bp], 10664999 duplicates)
Reads: 61116343 total, 48570 skipped (flags/unmapped)
Fragments: 30824511 total (30214422 tlen-paired, 2370 hash-paired, 380 singletons, 11736 discordant, 595603 orphans, 7367 too large [>5000 bp], 12478183 duplicates)
Reads: 66245695 total, 48294 skipped (flags/unmapped)
Fragments: 33413128 total (32730251 tlen-paired, 3917 hash-paired, 297 singletons, 11131 discordant, 667532 orphans, 19487 too large [>5000 bp], 13544320 duplicates)
Reads: 68430917 total, 79244 skipped (flags/unmapped)
Fragments: 34790783 total (32788014 tlen-paired, 2524 hash-paired, 366 singletons, 388002 discordant, 1611877 orphans, 191175 too large [>5000 bp], 13868252 duplicates)