Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/1e2a93321152b2926984c2b4994a18/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_5JZ-N1-BDNA-1_A23H3NYLT3_1/1136_5JZ-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  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/42/1e2a93321152b2926984c2b4994a18/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_5JZ-N1-BDNA-1_A23H3NYLT3_1/1136_5JZ-N1-BDNA-1_A23H3NYLT3_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: 1136_5JZ-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_5JZ-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_5JZ-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_5JZ-N1-BDNA-1_A23H3NYLT3_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: 104892352 total, 87548 skipped (flags/unmapped)
Fragments: 52634912 total (52107457 tlen-paired, 24255 hash-paired, 9996 singletons, 9478 discordant, 483726 orphans, 14351 too large [>5000 bp], 7613091 duplicates)
Reads: 113317761 total, 79485 skipped (flags/unmapped)
Fragments: 56878916 total (56284206 tlen-paired, 25675 hash-paired, 10426 singletons, 10053 discordant, 548556 orphans, 19713 too large [>5000 bp], 8172072 duplicates)
Reads: 113885984 total, 75017 skipped (flags/unmapped)
Fragments: 57178099 total (56571437 tlen-paired, 25725 hash-paired, 10339 singletons, 7864 discordant, 562734 orphans, 13921 too large [>5000 bp], 8201881 duplicates)
Reads: 114663591 total, 129366 skipped (flags/unmapped)
Fragments: 57850544 total (56051680 tlen-paired, 24461 hash-paired, 10774 singletons, 344584 discordant, 1419045 orphans, 131478 too large [>5000 bp], 8217260 duplicates)