Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_TWA-N1-BDNA-1_B23MHTGLT4_1/1029_TWA-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/1029_TWA-N1-BDNA-1_B23MHTGLT4_1/1029_TWA-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/6c0b5572bae9bb7f425ce5db58833e/.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/ed/6c0b5572bae9bb7f425ce5db58833e/.command.run
==> 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: 1029_TWA-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1029_TWA-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_TWA-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_TWA-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: 82154419 total, 50536 skipped (flags/unmapped)
Fragments: 41194815 total (40882107 tlen-paired, 2035 hash-paired, 566 singletons, 8606 discordant, 301501 orphans, 8160 too large [>5000 bp], 11945199 duplicates)
Reads: 78035970 total, 59332 skipped (flags/unmapped)
Fragments: 39127580 total (38812655 tlen-paired, 3238 hash-paired, 518 singletons, 12903 discordant, 298266 orphans, 10131 too large [>5000 bp], 11604289 duplicates)
Reads: 89948580 total, 54374 skipped (flags/unmapped)
Fragments: 45105955 total (44726419 tlen-paired, 2534 hash-paired, 472 singletons, 13626 discordant, 362904 orphans, 22836 too large [>5000 bp], 13415767 duplicates)
Reads: 90536941 total, 94398 skipped (flags/unmapped)
Fragments: 45513647 total (44592457 tlen-paired, 3881 hash-paired, 523 singletons, 176102 discordant, 740684 orphans, 78228 too large [>5000 bp], 13568760 duplicates)