Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_2S9-N1-BDNA-1_A237CFYLT3_1/1136_2S9-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/500a78e14a0ee83305f9380b6a5870/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_2S9-N1-BDNA-1_A237CFYLT3_1/1136_2S9-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  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/ab/500a78e14a0ee83305f9380b6a5870/.command.run
==> 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_2S9-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2S9-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2S9-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2S9-N1-BDNA-1_A237CFYLT3_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: 97028739 total, 105620 skipped (flags/unmapped)
Fragments: 48850875 total (48038015 tlen-paired, 7387 hash-paired, 15859 singletons, 13728 discordant, 775886 orphans, 6557 too large [>5000 bp], 11069370 duplicates)
Reads: 105989920 total, 100718 skipped (flags/unmapped)
Fragments: 53374715 total (52470304 tlen-paired, 8085 hash-paired, 16986 singletons, 10098 discordant, 869242 orphans, 13000 too large [>5000 bp], 12072011 duplicates)
Reads: 107447053 total, 104080 skipped (flags/unmapped)
Fragments: 54100719 total (53168565 tlen-paired, 9585 hash-paired, 17089 singletons, 14560 discordant, 890920 orphans, 24772 too large [>5000 bp], 12205975 duplicates)
Reads: 111164725 total, 238806 skipped (flags/unmapped)
Fragments: 56397107 total (53506482 tlen-paired, 8527 hash-paired, 17743 singletons, 560553 discordant, 2303802 orphans, 226625 too large [>5000 bp], 12541618 duplicates)