Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/874019346e4703ca2e6fca6d7d38ee/.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/e9/874019346e4703ca2e6fca6d7d38ee/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_7B-N1-BDNA-1_B23MHTGLT4_1/1136_7B-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_7B-N1-BDNA-1_B23MHTGLT4_1/1136_7B-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: 1136_7B-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7B-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7B-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7B-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: 89767597 total, 52049 skipped (flags/unmapped)
Fragments: 45087575 total (44593903 tlen-paired, 2845 hash-paired, 563 singletons, 10163 discordant, 480101 orphans, 10531 too large [>5000 bp], 14971845 duplicates)
Reads: 85565745 total, 63055 skipped (flags/unmapped)
Fragments: 42971977 total (42488129 tlen-paired, 3281 hash-paired, 446 singletons, 14649 discordant, 465472 orphans, 12327 too large [>5000 bp], 14574685 duplicates)
Reads: 98881533 total, 58464 skipped (flags/unmapped)
Fragments: 49668153 total (49084096 tlen-paired, 4075 hash-paired, 430 singletons, 14727 discordant, 564825 orphans, 26009 too large [>5000 bp], 16867205 duplicates)
Reads: 100498232 total, 100531 skipped (flags/unmapped)
Fragments: 50697984 total (49131240 tlen-paired, 3233 hash-paired, 461 singletons, 307634 discordant, 1255416 orphans, 128805 too large [>5000 bp], 17172476 duplicates)