Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_DQI-N1-BDNA-1_B23H2GYLT3_1/1029_DQI-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_DQI-N1-BDNA-1_B23H2GYLT3_1/1029_DQI-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/f806606c613b895b0c0c99d05eb348/.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/03/f806606c613b895b0c0c99d05eb348/.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: 1029_DQI-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DQI-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DQI-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DQI-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: 46185582 total, 40167 skipped (flags/unmapped)
Fragments: 23200358 total (22923452 tlen-paired, 5928 hash-paired, 3844 singletons, 4893 discordant, 262241 orphans, 5392 too large [>5000 bp], 4362899 duplicates)
Reads: 50669636 total, 37495 skipped (flags/unmapped)
Fragments: 25460186 total (25143405 tlen-paired, 6347 hash-paired, 4282 singletons, 5115 discordant, 301037 orphans, 8544 too large [>5000 bp], 4739984 duplicates)
Reads: 50363179 total, 34406 skipped (flags/unmapped)
Fragments: 25309801 total (24998843 tlen-paired, 6376 hash-paired, 3972 singletons, 3603 discordant, 297007 orphans, 5075 too large [>5000 bp], 4729928 duplicates)
Reads: 52098091 total, 60901 skipped (flags/unmapped)
Fragments: 26334954 total (25357948 tlen-paired, 6727 hash-paired, 4362 singletons, 190015 discordant, 775902 orphans, 73773 too large [>5000 bp], 4853313 duplicates)