Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_rr-N1-BDNA-1_A23TNVNLT4_1/659_rr-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_rr-N1-BDNA-1_A23TNVNLT4_1/659_rr-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/bdb6c905b52ce894dbc5190d25b403/.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/8b/bdb6c905b52ce894dbc5190d25b403/.command.run
==> 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_rr-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_rr-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_rr-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_rr-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: 88681545 total, 61706 skipped (flags/unmapped)
Fragments: 44485852 total (44093204 tlen-paired, 4029 hash-paired, 418 singletons, 16148 discordant, 372053 orphans, 10303 too large [>5000 bp], 15429097 duplicates)
Reads: 96518822 total, 50064 skipped (flags/unmapped)
Fragments: 48423735 total (48011928 tlen-paired, 3990 hash-paired, 530 singletons, 11637 discordant, 395650 orphans, 8734 too large [>5000 bp], 16485141 duplicates)
Reads: 94869700 total, 53435 skipped (flags/unmapped)
Fragments: 47599363 total (47166738 tlen-paired, 5469 hash-paired, 306 singletons, 13929 discordant, 412921 orphans, 15383 too large [>5000 bp], 16660737 duplicates)
Reads: 105651494 total, 99087 skipped (flags/unmapped)
Fragments: 53154236 total (51971670 tlen-paired, 3569 hash-paired, 406 singletons, 236868 discordant, 941723 orphans, 93032 too large [>5000 bp], 18550194 duplicates)