Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/a1126ac3409e786d73b31aa0f813ed/.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/79/a1126ac3409e786d73b31aa0f813ed/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_SX3-N1-BDNA-1_B23MHTGLT4_1/1029_SX3-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_SX3-N1-BDNA-1_B23MHTGLT4_1/1029_SX3-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
==> 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_SX3-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_SX3-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_SX3-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_SX3-N1-BDNA-1_B23MHTGLT4_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: 69070676 total, 55464 skipped (flags/unmapped)
Fragments: 34677775 total (34300754 tlen-paired, 3681 hash-paired, 420 singletons, 13484 discordant, 359436 orphans, 9759 too large [>5000 bp], 11100180 duplicates)
Reads: 72897882 total, 48384 skipped (flags/unmapped)
Fragments: 36607305 total (36200331 tlen-paired, 2614 hash-paired, 347 singletons, 11234 discordant, 392779 orphans, 14007 too large [>5000 bp], 11785725 duplicates)
Reads: 73240885 total, 44769 skipped (flags/unmapped)
Fragments: 36774647 total (36393676 tlen-paired, 1986 hash-paired, 401 singletons, 9183 discordant, 369401 orphans, 8312 too large [>5000 bp], 11508988 duplicates)
Reads: 80749088 total, 81899 skipped (flags/unmapped)
Fragments: 40697750 total (39550436 tlen-paired, 3778 hash-paired, 416 singletons, 227829 discordant, 915291 orphans, 93698 too large [>5000 bp], 13092421 duplicates)