Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/97a72f2db17541a3cf3400024f96f7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_1QF-N1-BDNA-1_A23KFG7LT4_1/1136_1QF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  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/7f/97a72f2db17541a3cf3400024f96f7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_1QF-N1-BDNA-1_A23KFG7LT4_1/1136_1QF-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] The index file is older than the data file: 1136_1QF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1QF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1QF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1QF-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: 80510789 total, 51323 skipped (flags/unmapped)
Fragments: 40340882 total (40079491 tlen-paired, 3046 hash-paired, 375 singletons, 14551 discordant, 243419 orphans, 10748 too large [>5000 bp], 13546428 duplicates)
Reads: 86551134 total, 44634 skipped (flags/unmapped)
Fragments: 43369935 total (43105138 tlen-paired, 3082 hash-paired, 431 singletons, 10231 discordant, 251053 orphans, 9057 too large [>5000 bp], 14120992 duplicates)
Reads: 85235609 total, 46490 skipped (flags/unmapped)
Fragments: 42713696 total (42430368 tlen-paired, 6158 hash-paired, 368 singletons, 11821 discordant, 264981 orphans, 13538 too large [>5000 bp], 14341178 duplicates)
Reads: 94344870 total, 77164 skipped (flags/unmapped)
Fragments: 47352004 total (46681751 tlen-paired, 1817 hash-paired, 397 singletons, 127990 discordant, 540049 orphans, 52072 too large [>5000 bp], 15948567 duplicates)