Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_LT1-N1-BDNA-1_B2377KTLT3_3/869_LT1-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_LT1-N1-BDNA-1_B2377KTLT3_3/869_LT1-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/58448386a01518ff7855c342f1d7c4/.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/c3/58448386a01518ff7855c342f1d7c4/.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: 869_LT1-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_LT1-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_LT1-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_LT1-N1-BDNA-1_B2377KTLT3_3.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: 105625965 total, 105984 skipped (flags/unmapped)
Fragments: 52927866 total (52498871 tlen-paired, 45306 hash-paired, 6772 singletons, 10512 discordant, 366405 orphans, 18713 too large [>5000 bp], 13363008 duplicates)
Reads: 106440253 total, 80182 skipped (flags/unmapped)
Fragments: 53367563 total (52905037 tlen-paired, 44167 hash-paired, 6662 singletons, 9344 discordant, 402353 orphans, 16980 too large [>5000 bp], 13406059 duplicates)
Reads: 118553376 total, 146795 skipped (flags/unmapped)
Fragments: 59603043 total (58316287 tlen-paired, 50268 hash-paired, 7638 singletons, 239377 discordant, 989473 orphans, 98803 too large [>5000 bp], 14903161 duplicates)
Reads: 118319302 total, 82691 skipped (flags/unmapped)
Fragments: 59313571 total (58843967 tlen-paired, 45352 hash-paired, 7400 singletons, 8031 discordant, 408821 orphans, 12845 too large [>5000 bp], 14939208 duplicates)