Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/005df48dd69a09aa1b549cb4238ce0/.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/63/005df48dd69a09aa1b549cb4238ce0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1136_03N-N1-BDNA-1_B23H2GYLT3_1/1136_03N-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/1136_03N-N1-BDNA-1_B23H2GYLT3_1/1136_03N-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: 1136_03N-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_03N-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_03N-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_03N-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: 62358084 total, 59878 skipped (flags/unmapped)
Fragments: 31302994 total (30962628 tlen-paired, 10015 hash-paired, 5353 singletons, 6897 discordant, 318101 orphans, 7836 too large [>5000 bp], 5898071 duplicates)
Reads: 68229566 total, 51478 skipped (flags/unmapped)
Fragments: 34266859 total (33880246 tlen-paired, 10784 hash-paired, 5635 singletons, 5115 discordant, 365079 orphans, 7542 too large [>5000 bp], 6462808 duplicates)
Reads: 68698720 total, 53642 skipped (flags/unmapped)
Fragments: 34500359 total (34103225 tlen-paired, 11633 hash-paired, 5783 singletons, 6889 discordant, 372829 orphans, 11486 too large [>5000 bp], 6468819 duplicates)
Reads: 69889831 total, 89789 skipped (flags/unmapped)
Fragments: 35283661 total (34105376 tlen-paired, 12163 hash-paired, 5947 singletons, 224874 discordant, 935301 orphans, 86984 too large [>5000 bp], 6538320 duplicates)