Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1173_Q7O-N1-BDNA-01_A23KFG7LT4_1/1173_Q7O-N1-BDNA-01_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/79f334934c8f69e9b815708e54e772/.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/10/79f334934c8f69e9b815708e54e772/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1173_Q7O-N1-BDNA-01_A23KFG7LT4_1/1173_Q7O-N1-BDNA-01_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] The index file is older than the data file: 1173_Q7O-N1-BDNA-01_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_Q7O-N1-BDNA-01_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_Q7O-N1-BDNA-01_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_Q7O-N1-BDNA-01_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: 68292427 total, 47332 skipped (flags/unmapped)
Fragments: 34221651 total (33993735 tlen-paired, 2772 hash-paired, 345 singletons, 11343 discordant, 213456 orphans, 7797 too large [>5000 bp], 12275811 duplicates)
Reads: 73161051 total, 40913 skipped (flags/unmapped)
Fragments: 36664807 total (36429662 tlen-paired, 2770 hash-paired, 341 singletons, 8019 discordant, 224015 orphans, 7440 too large [>5000 bp], 12761163 duplicates)
Reads: 72484067 total, 44429 skipped (flags/unmapped)
Fragments: 36324190 total (36068759 tlen-paired, 5145 hash-paired, 287 singletons, 9922 discordant, 240077 orphans, 15811 too large [>5000 bp], 13060456 duplicates)
Reads: 79797266 total, 65715 skipped (flags/unmapped)
Fragments: 40065495 total (39445897 tlen-paired, 2346 hash-paired, 322 singletons, 119765 discordant, 497165 orphans, 49024 too large [>5000 bp], 14464035 duplicates)