Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BCTD-N1-BDNA-1_B23H2GYLT3_1/1029_BCTD-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BCTD-N1-BDNA-1_B23H2GYLT3_1/1029_BCTD-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/bafc325a2266f3c6c3d4f16e252121/.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/fd/bafc325a2266f3c6c3d4f16e252121/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BCTD-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BCTD-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BCTD-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCTD-N1-BDNA-1_B23H2GYLT3_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: 79879072 total, 70664 skipped (flags/unmapped)
Fragments: 40091548 total (39678279 tlen-paired, 14752 hash-paired, 6455 singletons, 8541 discordant, 383521 orphans, 7644 too large [>5000 bp], 8297602 duplicates)
Reads: 88196995 total, 60269 skipped (flags/unmapped)
Fragments: 44285333 total (43813973 tlen-paired, 15545 hash-paired, 6736 singletons, 5851 discordant, 443228 orphans, 8012 too large [>5000 bp], 9138870 duplicates)
Reads: 88561817 total, 63799 skipped (flags/unmapped)
Fragments: 44462355 total (43998820 tlen-paired, 15997 hash-paired, 6831 singletons, 8146 discordant, 432561 orphans, 6350 too large [>5000 bp], 9178774 duplicates)
Reads: 89975665 total, 108147 skipped (flags/unmapped)
Fragments: 45396908 total (43964477 tlen-paired, 15718 hash-paired, 7132 singletons, 275883 discordant, 1133698 orphans, 107266 too large [>5000 bp], 9294076 duplicates)