Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_H9-N1-BDNA-1_B23H3Y2LT3_1/869_H9-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/a54f8dac66a2b26ba2ed2ba11b264a/.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/31/a54f8dac66a2b26ba2ed2ba11b264a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_H9-N1-BDNA-1_B23H3Y2LT3_1/869_H9-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam
==> 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: 869_H9-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_H9-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_H9-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_H9-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: 92210059 total, 94471 skipped (flags/unmapped)
Fragments: 46345534 total (45722786 tlen-paired, 12921 hash-paired, 3226 singletons, 10691 discordant, 595910 orphans, 11828 too large [>5000 bp], 10328442 duplicates)
Reads: 100878304 total, 78577 skipped (flags/unmapped)
Fragments: 50724905 total (50034502 tlen-paired, 11697 hash-paired, 3383 singletons, 7861 discordant, 667462 orphans, 10381 too large [>5000 bp], 11265542 duplicates)
Reads: 101553550 total, 79943 skipped (flags/unmapped)
Fragments: 51062085 total (50350111 tlen-paired, 14391 hash-paired, 3378 singletons, 11046 discordant, 683159 orphans, 17987 too large [>5000 bp], 11262808 duplicates)
Reads: 104752303 total, 206606 skipped (flags/unmapped)
Fragments: 52987378 total (50774416 tlen-paired, 13120 hash-paired, 3727 singletons, 427755 discordant, 1768360 orphans, 171514 too large [>5000 bp], 11562252 duplicates)