Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_5EQ-N1-BDNA-1_B23L5TMLT4_1/1136_5EQ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_5EQ-N1-BDNA-1_B23L5TMLT4_1/1136_5EQ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/8926e220e324cb53d3a7c233451dac/.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/c3/8926e220e324cb53d3a7c233451dac/.command.run
==> 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: 1136_5EQ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5EQ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5EQ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_5EQ-N1-BDNA-1_B23L5TMLT4_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: 74481910 total, 42430 skipped (flags/unmapped)
Fragments: 37405480 total (37008133 tlen-paired, 2216 hash-paired, 487 singletons, 7197 discordant, 387447 orphans, 8227 too large [>5000 bp], 13149392 duplicates)
Reads: 69807589 total, 50548 skipped (flags/unmapped)
Fragments: 35051652 total (34672720 tlen-paired, 3078 hash-paired, 401 singletons, 9941 discordant, 365512 orphans, 9825 too large [>5000 bp], 12581160 duplicates)
Reads: 73826679 total, 46003 skipped (flags/unmapped)
Fragments: 37074378 total (36651236 tlen-paired, 3891 hash-paired, 326 singletons, 9379 discordant, 409546 orphans, 20896 too large [>5000 bp], 13300376 duplicates)
Reads: 81869919 total, 83402 skipped (flags/unmapped)
Fragments: 41283704 total (40041993 tlen-paired, 3256 hash-paired, 471 singletons, 249686 discordant, 988298 orphans, 103939 too large [>5000 bp], 14738983 duplicates)