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/62/e43e3ef5155d1eb7c72bda2f1dc49a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/e43e3ef5155d1eb7c72bda2f1dc49a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_6Q8-N1-BDNA-1_A23KFG7LT4_1/1136_6Q8-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_6Q8-N1-BDNA-1_A23KFG7LT4_1/1136_6Q8-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_6Q8-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_6Q8-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_6Q8-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6Q8-N1-BDNA-1_A23KFG7LT4_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: 59803930 total, 43909 skipped (flags/unmapped)
Fragments: 30055931 total (29668166 tlen-paired, 2674 hash-paired, 350 singletons, 14606 discordant, 370135 orphans, 9322 too large [>5000 bp], 10532201 duplicates)
Reads: 63747928 total, 38817 skipped (flags/unmapped)
Fragments: 32036467 total (31642978 tlen-paired, 2690 hash-paired, 413 singletons, 9676 discordant, 380710 orphans, 8650 too large [>5000 bp], 10875320 duplicates)
Reads: 70835175 total, 63746 skipped (flags/unmapped)
Fragments: 35770581 total (34573052 tlen-paired, 1448 hash-paired, 402 singletons, 232982 discordant, 962697 orphans, 96683 too large [>5000 bp], 12483151 duplicates)
Reads: 69629911 total, 40624 skipped (flags/unmapped)
Fragments: 34998130 total (34548517 tlen-paired, 4216 hash-paired, 269 singletons, 14554 discordant, 430574 orphans, 11935 too large [>5000 bp], 12256761 duplicates)