Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/81b028dc5c42d9c7773b17dc1ea201/.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/10/81b028dc5c42d9c7773b17dc1ea201/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_I2Q-N1-BDNA-1_B23H2GYLT3_1/1029_I2Q-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_I2Q-N1-BDNA-1_B23H2GYLT3_1/1029_I2Q-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
==> 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_I2Q-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I2Q-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I2Q-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I2Q-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: 38892447 total, 33270 skipped (flags/unmapped)
Fragments: 19515654 total (19325354 tlen-paired, 7490 hash-paired, 2847 singletons, 4101 discordant, 175862 orphans, 3289 too large [>5000 bp], 3127603 duplicates)
Reads: 39229738 total, 29890 skipped (flags/unmapped)
Fragments: 19687367 total (19490390 tlen-paired, 8090 hash-paired, 2833 singletons, 3565 discordant, 182489 orphans, 5218 too large [>5000 bp], 3126506 duplicates)
Reads: 42808252 total, 29949 skipped (flags/unmapped)
Fragments: 21487134 total (21271091 tlen-paired, 8530 hash-paired, 2974 singletons, 3066 discordant, 201473 orphans, 4241 too large [>5000 bp], 3409089 duplicates)
Reads: 43526423 total, 54097 skipped (flags/unmapped)
Fragments: 21937219 total (21304543 tlen-paired, 8244 hash-paired, 3202 singletons, 123732 discordant, 497498 orphans, 49294 too large [>5000 bp], 3453623 duplicates)