Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/19ceed167e3bc2ba0f16864b36b0c3/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_PC8-N1-BDNA-1_B23MHTGLT4_1/1029_PC8-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_PC8-N1-BDNA-1_B23MHTGLT4_1/1029_PC8-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  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/7f/19ceed167e3bc2ba0f16864b36b0c3/.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_PC8-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_PC8-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_PC8-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_PC8-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: 56749138 total, 44913 skipped (flags/unmapped)
Fragments: 28484258 total (28190775 tlen-paired, 3405 hash-paired, 334 singletons, 10765 discordant, 278979 orphans, 7511 too large [>5000 bp], 7697156 duplicates)
Reads: 59818685 total, 38122 skipped (flags/unmapped)
Fragments: 30030694 total (29714532 tlen-paired, 3498 hash-paired, 312 singletons, 9289 discordant, 303063 orphans, 11275 too large [>5000 bp], 8167213 duplicates)
Reads: 61053695 total, 35851 skipped (flags/unmapped)
Fragments: 30647962 total (30346664 tlen-paired, 2524 hash-paired, 422 singletons, 7630 discordant, 290722 orphans, 6532 too large [>5000 bp], 8120113 duplicates)
Reads: 66000249 total, 68103 skipped (flags/unmapped)
Fragments: 33247638 total (32361146 tlen-paired, 2213 hash-paired, 368 singletons, 174583 discordant, 709328 orphans, 73283 too large [>5000 bp], 9012908 duplicates)