Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/cd11a3928f4b3c92dfa984e48b876c/.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/71/cd11a3928f4b3c92dfa984e48b876c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_4UT-N1-BDNA-1_B23MHTGLT4_1/1136_4UT-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/1136_4UT-N1-BDNA-1_B23MHTGLT4_1/1136_4UT-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: 1136_4UT-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4UT-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_4UT-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4UT-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: 54199077 total, 35917 skipped (flags/unmapped)
Fragments: 27224988 total (26898521 tlen-paired, 2528 hash-paired, 239 singletons, 9715 discordant, 313985 orphans, 13704 too large [>5000 bp], 7689444 duplicates)
Reads: 55032907 total, 33486 skipped (flags/unmapped)
Fragments: 27640110 total (27336208 tlen-paired, 1950 hash-paired, 347 singletons, 7681 discordant, 293924 orphans, 6736 too large [>5000 bp], 7610121 duplicates)
Reads: 51379608 total, 39675 skipped (flags/unmapped)
Fragments: 25803352 total (25508426 tlen-paired, 1857 hash-paired, 307 singletons, 11046 discordant, 281716 orphans, 7626 too large [>5000 bp], 7279167 duplicates)
Reads: 59849906 total, 57552 skipped (flags/unmapped)
Fragments: 30182422 total (29284379 tlen-paired, 1647 hash-paired, 343 singletons, 177390 discordant, 718663 orphans, 73258 too large [>5000 bp], 8499297 duplicates)