Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_W8F-N1-BDNA-1_B23MHTGLT4_1/1029_W8F-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/b79110c116b246da7d56a2a5242bbf/.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/d9/b79110c116b246da7d56a2a5242bbf/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_W8F-N1-BDNA-1_B23MHTGLT4_1/1029_W8F-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] [W::hts_idx_load3] The index file is older than the data file: 1029_W8F-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_W8F-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_W8F-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_W8F-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: 70164245 total, 53428 skipped (flags/unmapped)
Fragments: 35246967 total (34827950 tlen-paired, 3006 hash-paired, 437 singletons, 10850 discordant, 404724 orphans, 11022 too large [>5000 bp], 10886155 duplicates)
Reads: 74203077 total, 46406 skipped (flags/unmapped)
Fragments: 37286386 total (36837961 tlen-paired, 3542 hash-paired, 358 singletons, 9072 discordant, 435453 orphans, 9855 too large [>5000 bp], 11540217 duplicates)
Reads: 75301184 total, 46716 skipped (flags/unmapped)
Fragments: 37831563 total (37391036 tlen-paired, 2748 hash-paired, 524 singletons, 7669 discordant, 429586 orphans, 10726 too large [>5000 bp], 11381379 duplicates)
Reads: 82548628 total, 81904 skipped (flags/unmapped)
Fragments: 41673876 total (40282514 tlen-paired, 2567 hash-paired, 482 singletons, 280233 discordant, 1108080 orphans, 113767 too large [>5000 bp], 12823819 duplicates)