Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/a5ca1df164658c06894c87263a06e2/.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/3f/a5ca1df164658c06894c87263a06e2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BTVD-N1-BDNA-1_A23TNVNLT4_1/1241_BTVD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BTVD-N1-BDNA-1_A23TNVNLT4_1/1241_BTVD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
==> 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: 1241_BTVD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_BTVD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_BTVD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1241_BTVD-N1-BDNA-1_A23TNVNLT4_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: 84553101 total, 52973 skipped (flags/unmapped)
Fragments: 42374215 total (42093276 tlen-paired, 3325 hash-paired, 397 singletons, 12218 discordant, 264999 orphans, 8547 too large [>5000 bp], 15103620 duplicates)
Reads: 90487618 total, 43909 skipped (flags/unmapped)
Fragments: 45353104 total (45064768 tlen-paired, 2498 hash-paired, 442 singletons, 8107 discordant, 277289 orphans, 7616 too large [>5000 bp], 15861629 duplicates)
Reads: 100164674 total, 83478 skipped (flags/unmapped)
Fragments: 50310577 total (49472897 tlen-paired, 2808 hash-paired, 428 singletons, 163082 discordant, 671362 orphans, 65916 too large [>5000 bp], 18057282 duplicates)
Reads: 98497714 total, 49065 skipped (flags/unmapped)
Fragments: 49367630 total (49029145 tlen-paired, 3443 hash-paired, 378 singletons, 12061 discordant, 322603 orphans, 18185 too large [>5000 bp], 17706876 duplicates)