Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/b9c6729ffd29e7c0861fe89e8159a1/.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/ab/b9c6729ffd29e7c0861fe89e8159a1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_83H-N1-BDNA-1_A23NMNVLT4_1/1136_83H-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_83H-N1-BDNA-1_A23NMNVLT4_1/1136_83H-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

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: 1136_83H-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_83H-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_83H-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_83H-N1-BDNA-1_A23NMNVLT4_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: 34265039 total, 24513 skipped (flags/unmapped)
Fragments: 17172737 total (17055148 tlen-paired, 1764 hash-paired, 133 singletons, 4593 discordant, 111099 orphans, 3142 too large [>5000 bp], 4202505 duplicates)
Reads: 37335284 total, 19594 skipped (flags/unmapped)
Fragments: 18712144 total (18592191 tlen-paired, 1354 hash-paired, 141 singletons, 3291 discordant, 115167 orphans, 3355 too large [>5000 bp], 4460770 duplicates)
Reads: 40662735 total, 21641 skipped (flags/unmapped)
Fragments: 20380950 total (20242045 tlen-paired, 1368 hash-paired, 142 singletons, 4783 discordant, 132612 orphans, 5974 too large [>5000 bp], 5021477 duplicates)
Reads: 40836290 total, 37592 skipped (flags/unmapped)
Fragments: 20513438 total (20157500 tlen-paired, 1636 hash-paired, 164 singletons, 69100 discordant, 285038 orphans, 28512 too large [>5000 bp], 5054349 duplicates)