Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/53a5dfe579e621ce83d56cd5641af7/.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/df/53a5dfe579e621ce83d56cd5641af7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_H3N-N1-BDNA-1_B23MHTGLT4_1/1029_H3N-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_H3N-N1-BDNA-1_B23MHTGLT4_1/1029_H3N-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
==> 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: 1029_H3N-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_H3N-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H3N-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H3N-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: 66016793 total, 53137 skipped (flags/unmapped)
Fragments: 33114250 total (32813083 tlen-paired, 3727 hash-paired, 434 singletons, 12352 discordant, 284654 orphans, 10122 too large [>5000 bp], 10013852 duplicates)
Reads: 69714952 total, 44314 skipped (flags/unmapped)
Fragments: 34972210 total (34669261 tlen-paired, 2957 hash-paired, 363 singletons, 8354 discordant, 291275 orphans, 8928 too large [>5000 bp], 10366905 duplicates)
Reads: 76069143 total, 47053 skipped (flags/unmapped)
Fragments: 38164852 total (37806394 tlen-paired, 2771 hash-paired, 367 singletons, 12721 discordant, 342599 orphans, 17676 too large [>5000 bp], 11552544 duplicates)
Reads: 76876990 total, 72929 skipped (flags/unmapped)
Fragments: 38687645 total (37805091 tlen-paired, 2087 hash-paired, 434 singletons, 169308 discordant, 710725 orphans, 69965 too large [>5000 bp], 11705413 duplicates)