Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/a0d07a0e0dc58451c0286fcf900ef0/.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/72/a0d07a0e0dc58451c0286fcf900ef0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_RCF-N1-BDNA-1_B23H2GYLT3_1/1029_RCF-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_RCF-N1-BDNA-1_B23H2GYLT3_1/1029_RCF-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_RCF-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_RCF-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_RCF-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_RCF-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: 82895469 total, 69878 skipped (flags/unmapped)
Fragments: 41587994 total (41192983 tlen-paired, 18908 hash-paired, 5948 singletons, 8640 discordant, 361515 orphans, 8533 too large [>5000 bp], 8920099 duplicates)
Reads: 83317254 total, 59279 skipped (flags/unmapped)
Fragments: 41812025 total (41396749 tlen-paired, 19063 hash-paired, 5976 singletons, 6944 discordant, 383293 orphans, 11597 too large [>5000 bp], 8910600 duplicates)
Reads: 90955147 total, 59949 skipped (flags/unmapped)
Fragments: 45648158 total (45202029 tlen-paired, 18883 hash-paired, 6450 singletons, 6248 discordant, 414548 orphans, 9940 too large [>5000 bp], 9745376 duplicates)
Reads: 92654637 total, 103770 skipped (flags/unmapped)
Fragments: 46691743 total (45386697 tlen-paired, 21028 hash-paired, 6557 singletons, 251683 discordant, 1025778 orphans, 99858 too large [>5000 bp], 9883593 duplicates)