Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/06fffdd98c711e2faedb5e0951c2f0/.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/56/06fffdd98c711e2faedb5e0951c2f0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_URF-N1-BDNA-1_B23MHTGLT4_1/1029_URF-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_URF-N1-BDNA-1_B23MHTGLT4_1/1029_URF-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_URF-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_URF-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_URF-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_URF-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: 97628534 total, 72943 skipped (flags/unmapped)
Fragments: 49072233 total (48437970 tlen-paired, 3694 hash-paired, 540 singletons, 17982 discordant, 612047 orphans, 11856 too large [>5000 bp], 17069202 duplicates)
Reads: 103895935 total, 61984 skipped (flags/unmapped)
Fragments: 52220605 total (51573269 tlen-paired, 3899 hash-paired, 668 singletons, 12106 discordant, 630663 orphans, 12036 too large [>5000 bp], 17813601 duplicates)
Reads: 113091405 total, 67243 skipped (flags/unmapped)
Fragments: 56846231 total (56118359 tlen-paired, 4961 hash-paired, 514 singletons, 17823 discordant, 704574 orphans, 18394 too large [>5000 bp], 19901400 duplicates)
Reads: 115195487 total, 106500 skipped (flags/unmapped)
Fragments: 58213646 total (56126884 tlen-paired, 2270 hash-paired, 569 singletons, 408407 discordant, 1675516 orphans, 168890 too large [>5000 bp], 20286746 duplicates)