Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/e6dfa2853fe7addc295797cd5f793c/.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/03/e6dfa2853fe7addc295797cd5f793c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_5TH-N1-BDNA-1_B23MHTGLT4_1/1136_5TH-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/1136_5TH-N1-BDNA-1_B23MHTGLT4_1/1136_5TH-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: 1136_5TH-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_5TH-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_5TH-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TH-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: 90786165 total, 67109 skipped (flags/unmapped)
Fragments: 45597738 total (45079641 tlen-paired, 3827 hash-paired, 529 singletons, 13900 discordant, 499841 orphans, 11975 too large [>5000 bp], 15320700 duplicates)
Reads: 96080698 total, 56153 skipped (flags/unmapped)
Fragments: 48260280 total (47729297 tlen-paired, 3236 hash-paired, 559 singletons, 9642 discordant, 517546 orphans, 11045 too large [>5000 bp], 15921890 duplicates)
Reads: 105484961 total, 63164 skipped (flags/unmapped)
Fragments: 52986336 total (52360878 tlen-paired, 3622 hash-paired, 476 singletons, 15005 discordant, 606355 orphans, 27978 too large [>5000 bp], 17870086 duplicates)
Reads: 106670992 total, 100877 skipped (flags/unmapped)
Fragments: 53834081 total (52112940 tlen-paired, 3191 hash-paired, 539 singletons, 336095 discordant, 1381316 orphans, 141904 too large [>5000 bp], 18122256 duplicates)