Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/9165ccebe5ba6922dda6c68b53b686/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_bV0-N1-BDNA-1_A23TY32LT4_1/659_bV0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  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/7b/9165ccebe5ba6922dda6c68b53b686/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_bV0-N1-BDNA-1_A23TY32LT4_1/659_bV0-N1-BDNA-1_A23TY32LT4_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: 659_bV0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bV0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bV0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bV0-N1-BDNA-1_A23TY32LT4_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: 91695995 total, 67398 skipped (flags/unmapped)
Fragments: 45983719 total (45599245 tlen-paired, 3901 hash-paired, 430 singletons, 15964 discordant, 364179 orphans, 12884 too large [>5000 bp], 19075251 duplicates)
Reads: 100223057 total, 57270 skipped (flags/unmapped)
Fragments: 50267556 total (49860865 tlen-paired, 3913 hash-paired, 529 singletons, 11509 discordant, 390740 orphans, 10972 too large [>5000 bp], 20444272 duplicates)
Reads: 99182881 total, 61770 skipped (flags/unmapped)
Fragments: 49751358 total (49296775 tlen-paired, 5354 hash-paired, 293 singletons, 14792 discordant, 434144 orphans, 26416 too large [>5000 bp], 20793317 duplicates)
Reads: 110394230 total, 107930 skipped (flags/unmapped)
Fragments: 55509959 total (54357558 tlen-paired, 4234 hash-paired, 402 singletons, 230953 discordant, 916812 orphans, 91798 too large [>5000 bp], 23130564 duplicates)