Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1047_CH-N1-BDNA-1_A23NLN3LT4_1/1047_CH-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/4356955450d77b69d5c5a1ac03941e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1047_CH-N1-BDNA-1_A23NLN3LT4_1/1047_CH-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  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/f3/4356955450d77b69d5c5a1ac03941e/.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: 1047_CH-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_CH-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_CH-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_CH-N1-BDNA-1_A23NLN3LT4_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: 80537934 total, 60125 skipped (flags/unmapped)
Fragments: 40362105 total (40064279 tlen-paired, 3159 hash-paired, 387 singletons, 20100 discordant, 274180 orphans, 14083 too large [>5000 bp], 14233710 duplicates)
Reads: 86888741 total, 47069 skipped (flags/unmapped)
Fragments: 43549208 total (43257248 tlen-paired, 2538 hash-paired, 416 singletons, 13534 discordant, 275472 orphans, 9572 too large [>5000 bp], 15147208 duplicates)
Reads: 94502139 total, 86016 skipped (flags/unmapped)
Fragments: 47434113 total (46749093 tlen-paired, 3080 hash-paired, 334 singletons, 126391 discordant, 555215 orphans, 51723 too large [>5000 bp], 16965421 duplicates)
Reads: 87733405 total, 54443 skipped (flags/unmapped)
Fragments: 43971615 total (43641319 tlen-paired, 3958 hash-paired, 347 singletons, 17786 discordant, 308205 orphans, 22142 too large [>5000 bp], 15702344 duplicates)