Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/659_ebP-N1-BDNA-1_B23H3Y2LT3_1/659_ebP-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/fdc83d57fe8812c69321a81c6fef71/.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/bd/fdc83d57fe8812c69321a81c6fef71/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/659_ebP-N1-BDNA-1_B23H3Y2LT3_1/659_ebP-N1-BDNA-1_B23H3Y2LT3_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: 659_ebP-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ebP-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ebP-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ebP-N1-BDNA-1_B23H3Y2LT3_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: 82619804 total, 83543 skipped (flags/unmapped)
Fragments: 41527169 total (40969986 tlen-paired, 11471 hash-paired, 2729 singletons, 9009 discordant, 533974 orphans, 9313 too large [>5000 bp], 8963943 duplicates)
Reads: 82589377 total, 72030 skipped (flags/unmapped)
Fragments: 41523594 total (40941797 tlen-paired, 10327 hash-paired, 2644 singletons, 8055 discordant, 560771 orphans, 16787 too large [>5000 bp], 8914100 duplicates)
Reads: 91213606 total, 69515 skipped (flags/unmapped)
Fragments: 45865400 total (45244087 tlen-paired, 10361 hash-paired, 2927 singletons, 6577 discordant, 601448 orphans, 8833 too large [>5000 bp], 9843037 duplicates)
Reads: 94112333 total, 174740 skipped (flags/unmapped)
Fragments: 47590180 total (45629572 tlen-paired, 11414 hash-paired, 3050 singletons, 391715 discordant, 1554429 orphans, 157356 too large [>5000 bp], 10080461 duplicates)