Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_NK-N1-BDNA-1_B23MHTGLT4_1/1047_NK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/bfecb2cfa5a8eee737ab8b555da91b/.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/e3/bfecb2cfa5a8eee737ab8b555da91b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_NK-N1-BDNA-1_B23MHTGLT4_1/1047_NK-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: 1047_NK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1047_NK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1047_NK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_NK-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: 91216130 total, 67310 skipped (flags/unmapped)
Fragments: 45814294 total (45293858 tlen-paired, 3205 hash-paired, 534 singletons, 14451 discordant, 502246 orphans, 11506 too large [>5000 bp], 15469694 duplicates)
Reads: 97955181 total, 58834 skipped (flags/unmapped)
Fragments: 49198166 total (48658111 tlen-paired, 3824 hash-paired, 641 singletons, 9702 discordant, 525888 orphans, 13272 too large [>5000 bp], 16278127 duplicates)
Reads: 105450126 total, 63158 skipped (flags/unmapped)
Fragments: 52969614 total (52342190 tlen-paired, 5076 hash-paired, 505 singletons, 14764 discordant, 607079 orphans, 27662 too large [>5000 bp], 17995044 duplicates)
Reads: 107447803 total, 104429 skipped (flags/unmapped)
Fragments: 54222612 total (52498432 tlen-paired, 3351 hash-paired, 577 singletons, 337579 discordant, 1382673 orphans, 140700 too large [>5000 bp], 18357307 duplicates)