Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/e83314274f6a6082b0513d52e8813a/.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/dd/e83314274f6a6082b0513d52e8813a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1173_LAF-N1-BDNA-01_B23MHTGLT4_1/1173_LAF-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1173_LAF-N1-BDNA-01_B23MHTGLT4_1/1173_LAF-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
==> 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: 1173_LAF-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_LAF-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_LAF-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_LAF-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
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: 57457079 total, 43786 skipped (flags/unmapped)
Fragments: 28832297 total (28553319 tlen-paired, 2159 hash-paired, 283 singletons, 10630 discordant, 265906 orphans, 7444 too large [>5000 bp], 8531216 duplicates)
Reads: 61499617 total, 35888 skipped (flags/unmapped)
Fragments: 30860745 total (30577950 tlen-paired, 1976 hash-paired, 350 singletons, 7488 discordant, 272981 orphans, 7785 too large [>5000 bp], 8893718 duplicates)
Reads: 60216866 total, 40405 skipped (flags/unmapped)
Fragments: 30218070 total (29910303 tlen-paired, 3724 hash-paired, 283 singletons, 9264 discordant, 294496 orphans, 17550 too large [>5000 bp], 8949233 duplicates)
Reads: 67088534 total, 60915 skipped (flags/unmapped)
Fragments: 33776750 total (32949687 tlen-paired, 1886 hash-paired, 351 singletons, 163398 discordant, 661428 orphans, 67949 too large [>5000 bp], 10020850 duplicates)