Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_LPB-N1-BDNA-1_B23MHTGLT4_1/1029_LPB-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/0ca4c88054427f30b683c8bbb12a6a/.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/44/0ca4c88054427f30b683c8bbb12a6a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_LPB-N1-BDNA-1_B23MHTGLT4_1/1029_LPB-N1-BDNA-1_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] [W::hts_idx_load3] The index file is older than the data file: 1029_LPB-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_LPB-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_LPB-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_LPB-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: 45825853 total, 34857 skipped (flags/unmapped)
Fragments: 22996208 total (22773783 tlen-paired, 2383 hash-paired, 278 singletons, 8074 discordant, 211690 orphans, 5274 too large [>5000 bp], 6127611 duplicates)
Reads: 48857908 total, 29380 skipped (flags/unmapped)
Fragments: 24518706 total (24290856 tlen-paired, 1677 hash-paired, 297 singletons, 5325 discordant, 220551 orphans, 5982 too large [>5000 bp], 6386819 duplicates)
Reads: 48334902 total, 30926 skipped (flags/unmapped)
Fragments: 24259059 total (24021630 tlen-paired, 2043 hash-paired, 205 singletons, 6910 discordant, 228271 orphans, 7167 too large [>5000 bp], 6475361 duplicates)
Reads: 53408973 total, 52679 skipped (flags/unmapped)
Fragments: 26894402 total (26214586 tlen-paired, 1186 hash-paired, 292 singletons, 134338 discordant, 544000 orphans, 55891 too large [>5000 bp], 7161054 duplicates)