Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1047_JJ-N1-BDNA-1_A23NLN3LT4_1/1047_JJ-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/a36c878857492a9c08a0da8ad9ca09/.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/5b/a36c878857492a9c08a0da8ad9ca09/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1047_JJ-N1-BDNA-1_A23NLN3LT4_1/1047_JJ-N1-BDNA-1_A23NLN3LT4_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: 1047_JJ-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_JJ-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_JJ-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_JJ-N1-BDNA-1_A23NLN3LT4_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: 69922078 total, 49956 skipped (flags/unmapped)
Fragments: 35044274 total (34791116 tlen-paired, 3339 hash-paired, 283 singletons, 14665 discordant, 234871 orphans, 9364 too large [>5000 bp], 10867651 duplicates)
Reads: 75504711 total, 45344 skipped (flags/unmapped)
Fragments: 37847812 total (37553830 tlen-paired, 4159 hash-paired, 295 singletons, 13550 discordant, 275978 orphans, 20008 too large [>5000 bp], 11845255 duplicates)
Reads: 76686023 total, 41483 skipped (flags/unmapped)
Fragments: 38433510 total (38180936 tlen-paired, 2596 hash-paired, 400 singletons, 10496 discordant, 239082 orphans, 8501 too large [>5000 bp], 11696310 duplicates)
Reads: 82775807 total, 78356 skipped (flags/unmapped)
Fragments: 41551155 total (40923707 tlen-paired, 3443 hash-paired, 303 singletons, 118786 discordant, 504916 orphans, 50180 too large [>5000 bp], 13027077 duplicates)