Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_KOC-N1-BDNA-1_B23MHTGLT4_1/1029_KOC-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/3712d941aa7c2c0394dbe0f5d2af56/.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/37/3712d941aa7c2c0394dbe0f5d2af56/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_KOC-N1-BDNA-1_B23MHTGLT4_1/1029_KOC-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
==> 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_KOC-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_KOC-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_KOC-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_KOC-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: 72930796 total, 43778 skipped (flags/unmapped)
Fragments: 36585949 total (36273487 tlen-paired, 1822 hash-paired, 466 singletons, 9368 discordant, 300806 orphans, 8196 too large [>5000 bp], 10402579 duplicates)
Reads: 72295215 total, 51038 skipped (flags/unmapped)
Fragments: 36268450 total (35925265 tlen-paired, 2492 hash-paired, 353 singletons, 11512 discordant, 328828 orphans, 18229 too large [>5000 bp], 10559732 duplicates)
Reads: 68800642 total, 52462 skipped (flags/unmapped)
Fragments: 34512518 total (34202241 tlen-paired, 3620 hash-paired, 396 singletons, 13177 discordant, 293084 orphans, 8312 too large [>5000 bp], 10034177 duplicates)
Reads: 80143961 total, 87623 skipped (flags/unmapped)
Fragments: 40310193 total (39419961 tlen-paired, 2938 hash-paired, 414 singletons, 174316 discordant, 712564 orphans, 74465 too large [>5000 bp], 11738376 duplicates)