Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/0cf40e6622832d91d2278cb380eb8b/.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/36/0cf40e6622832d91d2278cb380eb8b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BGSQ-N1-BDNA-1_B23H2GYLT3_1/1029_BGSQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BGSQ-N1-BDNA-1_B23H2GYLT3_1/1029_BGSQ-N1-BDNA-1_B23H2GYLT3_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: 1029_BGSQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGSQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGSQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGSQ-N1-BDNA-1_B23H2GYLT3_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: 86040485 total, 76965 skipped (flags/unmapped)
Fragments: 43165469 total (42748435 tlen-paired, 22553 hash-paired, 5313 singletons, 8945 discordant, 380223 orphans, 9059 too large [>5000 bp], 9119226 duplicates)
Reads: 86892136 total, 64697 skipped (flags/unmapped)
Fragments: 43604963 total (43160028 tlen-paired, 21634 hash-paired, 5026 singletons, 7944 discordant, 410331 orphans, 16435 too large [>5000 bp], 9176999 duplicates)
Reads: 95334258 total, 64100 skipped (flags/unmapped)
Fragments: 47845113 total (47375365 tlen-paired, 22991 hash-paired, 5540 singletons, 6791 discordant, 434426 orphans, 9949 too large [>5000 bp], 10083765 duplicates)
Reads: 97008641 total, 118585 skipped (flags/unmapped)
Fragments: 48879030 total (47512135 tlen-paired, 24860 hash-paired, 5736 singletons, 266239 discordant, 1070060 orphans, 103896 too large [>5000 bp], 10241642 duplicates)