Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_67L-N1-BDNA-1_B23MHTGLT4_1/1136_67L-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/77c45ad691914a2ec31c4461fa2258/.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/fc/77c45ad691914a2ec31c4461fa2258/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_67L-N1-BDNA-1_B23MHTGLT4_1/1136_67L-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] The index file is older than the data file: 1136_67L-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_67L-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_67L-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_67L-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: 84961925 total, 80309 skipped (flags/unmapped)
Fragments: 42759827 total (42072568 tlen-paired, 4215 hash-paired, 523 singletons, 19370 discordant, 663151 orphans, 12818 too large [>5000 bp], 15549089 duplicates)
Reads: 89908086 total, 72110 skipped (flags/unmapped)
Fragments: 45257484 total (44508070 tlen-paired, 3218 hash-paired, 436 singletons, 17070 discordant, 728690 orphans, 25067 too large [>5000 bp], 16513502 duplicates)
Reads: 90594911 total, 69797 skipped (flags/unmapped)
Fragments: 45596327 total (44883863 tlen-paired, 2702 hash-paired, 556 singletons, 14450 discordant, 694756 orphans, 13886 too large [>5000 bp], 16226956 duplicates)
Reads: 101071054 total, 116325 skipped (flags/unmapped)
Fragments: 51182478 total (48945862 tlen-paired, 2314 hash-paired, 549 singletons, 451479 discordant, 1782274 orphans, 186298 too large [>5000 bp], 18520991 duplicates)