Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_7AL-N1-BDNA-1_B23H2GYLT3_1/1029_7AL-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/075cc3c70d45096d6580ba8e36fc0c/.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/a0/075cc3c70d45096d6580ba8e36fc0c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_7AL-N1-BDNA-1_B23H2GYLT3_1/1029_7AL-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
==> 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_7AL-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_7AL-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_7AL-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_7AL-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: 68296977 total, 58653 skipped (flags/unmapped)
Fragments: 34318667 total (33893344 tlen-paired, 5401 hash-paired, 5376 singletons, 4648 discordant, 409898 orphans, 8132 too large [>5000 bp], 6098730 duplicates)
Reads: 76016975 total, 53418 skipped (flags/unmapped)
Fragments: 38218257 total (37702516 tlen-paired, 6807 hash-paired, 5919 singletons, 5267 discordant, 497748 orphans, 15355 too large [>5000 bp], 6691122 duplicates)
Reads: 77751182 total, 94778 skipped (flags/unmapped)
Fragments: 39383426 total (37698876 tlen-paired, 6715 hash-paired, 6049 singletons, 339761 discordant, 1332025 orphans, 113813 too large [>5000 bp], 6795259 duplicates)
Reads: 76750990 total, 49774 skipped (flags/unmapped)
Fragments: 38608085 total (38069718 tlen-paired, 4694 hash-paired, 5841 singletons, 3709 discordant, 524123 orphans, 7505 too large [>5000 bp], 6772535 duplicates)