Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/f622ac91638b0e17d8997236dece7f/.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/fe/f622ac91638b0e17d8997236dece7f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_K2-N1-BDNA-1_B23MHTGLT4_1/1047_K2-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_K2-N1-BDNA-1_B23MHTGLT4_1/1047_K2-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_K2-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_K2-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_K2-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_K2-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: 77441719 total, 63099 skipped (flags/unmapped)
Fragments: 38929406 total (38412421 tlen-paired, 3615 hash-paired, 467 singletons, 14598 discordant, 498305 orphans, 9290 too large [>5000 bp], 12784381 duplicates)
Reads: 81786018 total, 52566 skipped (flags/unmapped)
Fragments: 41112498 total (40585956 tlen-paired, 2703 hash-paired, 521 singletons, 9909 discordant, 513409 orphans, 11193 too large [>5000 bp], 13260325 duplicates)
Reads: 89960772 total, 58554 skipped (flags/unmapped)
Fragments: 45224084 total (44625188 tlen-paired, 6268 hash-paired, 434 singletons, 15408 discordant, 576786 orphans, 15635 too large [>5000 bp], 14935959 duplicates)
Reads: 91340307 total, 96869 skipped (flags/unmapped)
Fragments: 46165685 total (44462806 tlen-paired, 2827 hash-paired, 486 singletons, 335014 discordant, 1364552 orphans, 138553 too large [>5000 bp], 15128882 duplicates)