Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0TE-N1-BDNA-1_A23KFG7LT4_1/1136_0TE-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/d6dc5cd153eb2dedc7645ff8ce03ed/.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/88/d6dc5cd153eb2dedc7645ff8ce03ed/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0TE-N1-BDNA-1_A23KFG7LT4_1/1136_0TE-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> 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: 1136_0TE-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0TE-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0TE-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0TE-N1-BDNA-1_A23KFG7LT4_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: 66059343 total, 43654 skipped (flags/unmapped)
Fragments: 33104035 total (32881609 tlen-paired, 2175 hash-paired, 375 singletons, 10934 discordant, 208942 orphans, 8468 too large [>5000 bp], 10853037 duplicates)
Reads: 77456731 total, 67137 skipped (flags/unmapped)
Fragments: 38891117 total (38278345 tlen-paired, 2186 hash-paired, 334 singletons, 119916 discordant, 490336 orphans, 49015 too large [>5000 bp], 12826067 duplicates)
Reads: 70256131 total, 41819 skipped (flags/unmapped)
Fragments: 35209942 total (34955768 tlen-paired, 5928 hash-paired, 284 singletons, 9322 discordant, 238640 orphans, 16676 too large [>5000 bp], 11567558 duplicates)
Reads: 71236837 total, 38514 skipped (flags/unmapped)
Fragments: 35699093 total (35471720 tlen-paired, 2874 hash-paired, 442 singletons, 7856 discordant, 216201 orphans, 8390 too large [>5000 bp], 11373028 duplicates)