Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_DB2-N1-BDNA-1_B23H2GYLT3_1/1029_DB2-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/d4f8773f47cbe05340be197d89eed0/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_DB2-N1-BDNA-1_B23H2GYLT3_1/1029_DB2-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  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/73/d4f8773f47cbe05340be197d89eed0/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_DB2-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DB2-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_DB2-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DB2-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: 79411041 total, 74756 skipped (flags/unmapped)
Fragments: 39838286 total (39454353 tlen-paired, 17625 hash-paired, 6494 singletons, 9017 discordant, 350797 orphans, 8502 too large [>5000 bp], 8297814 duplicates)
Reads: 79667141 total, 65378 skipped (flags/unmapped)
Fragments: 39978225 total (39571011 tlen-paired, 18290 hash-paired, 6787 singletons, 7841 discordant, 374296 orphans, 13198 too large [>5000 bp], 8267164 duplicates)
Reads: 87281410 total, 64946 skipped (flags/unmapped)
Fragments: 43803326 total (43370311 tlen-paired, 18094 hash-paired, 7067 singletons, 6773 discordant, 401081 orphans, 8980 too large [>5000 bp], 9070625 duplicates)
Reads: 88721513 total, 117801 skipped (flags/unmapped)
Fragments: 44701344 total (43455133 tlen-paired, 18651 hash-paired, 7456 singletons, 241074 discordant, 979030 orphans, 93755 too large [>5000 bp], 9198698 duplicates)