Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_Cc-N1-BDNA-1_A23TNVNLT4_1/659_Cc-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/1ed6621db8ea9e6af5d691d2e5f1af/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_Cc-N1-BDNA-1_A23TNVNLT4_1/659_Cc-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  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/f6/1ed6621db8ea9e6af5d691d2e5f1af/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_Cc-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Cc-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Cc-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_Cc-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: 75866153 total, 50391 skipped (flags/unmapped)
Fragments: 38028594 total (37750738 tlen-paired, 3926 hash-paired, 377 singletons, 13054 discordant, 260499 orphans, 9725 too large [>5000 bp], 13023101 duplicates)
Reads: 81707329 total, 41154 skipped (flags/unmapped)
Fragments: 40962200 total (40676916 tlen-paired, 3112 hash-paired, 428 singletons, 8981 discordant, 272763 orphans, 7483 too large [>5000 bp], 13714524 duplicates)
Reads: 81484497 total, 43591 skipped (flags/unmapped)
Fragments: 40851773 total (40539762 tlen-paired, 2991 hash-paired, 380 singletons, 11076 discordant, 297564 orphans, 17652 too large [>5000 bp], 14094164 duplicates)
Reads: 90742947 total, 82217 skipped (flags/unmapped)
Fragments: 45582854 total (44787450 tlen-paired, 4314 hash-paired, 417 singletons, 158180 discordant, 632493 orphans, 63966 too large [>5000 bp], 15728795 duplicates)