Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/83bf64d88c80fa3adea29cb0082ab6/.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/44/83bf64d88c80fa3adea29cb0082ab6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_GF-N1-BDNA-1_B23L5TMLT4_1/1047_GF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_GF-N1-BDNA-1_B23L5TMLT4_1/1047_GF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1047_GF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1047_GF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai

Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_GF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_GF-N1-BDNA-1_B23L5TMLT4_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: 89022005 total, 55545 skipped (flags/unmapped)
Fragments: 44680930 total (44251021 tlen-paired, 4239 hash-paired, 582 singletons, 10426 discordant, 414662 orphans, 9922 too large [>5000 bp], 17213971 duplicates)
Reads: 83794358 total, 65060 skipped (flags/unmapped)
Fragments: 42054805 total (41632199 tlen-paired, 4170 hash-paired, 494 singletons, 14872 discordant, 403070 orphans, 11626 too large [>5000 bp], 16459327 duplicates)
Reads: 99233475 total, 107338 skipped (flags/unmapped)
Fragments: 49980702 total (48670029 tlen-paired, 3729 hash-paired, 527 singletons, 255415 discordant, 1051002 orphans, 108131 too large [>5000 bp], 19537575 duplicates)
Reads: 97842677 total, 61195 skipped (flags/unmapped)
Fragments: 49107692 total (48600538 tlen-paired, 6434 hash-paired, 491 singletons, 15274 discordant, 484955 orphans, 25772 too large [>5000 bp], 19274251 duplicates)