Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/bbe859f9de58fa7c81063a0ba2613c/.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/8a/bbe859f9de58fa7c81063a0ba2613c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BZNT-N1-BDNA-1_A23TNVNLT4_1/1241_BZNT-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BZNT-N1-BDNA-1_A23TNVNLT4_1/1241_BZNT-N1-BDNA-1_A23TNVNLT4_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: 1241_BZNT-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BZNT-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BZNT-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BZNT-N1-BDNA-1_A23TNVNLT4_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: 49277443 total, 32924 skipped (flags/unmapped)
Fragments: 24702813 total (24522313 tlen-paired, 2457 hash-paired, 220 singletons, 8374 discordant, 169449 orphans, 4281 too large [>5000 bp], 7796961 duplicates)
Reads: 52778070 total, 28888 skipped (flags/unmapped)
Fragments: 26458216 total (26273049 tlen-paired, 2373 hash-paired, 263 singletons, 5592 discordant, 176939 orphans, 4976 too large [>5000 bp], 8194418 duplicates)
Reads: 57653264 total, 30373 skipped (flags/unmapped)
Fragments: 28902595 total (28687662 tlen-paired, 2115 hash-paired, 209 singletons, 8681 discordant, 203928 orphans, 10919 too large [>5000 bp], 9151559 duplicates)
Reads: 58552220 total, 53953 skipped (flags/unmapped)
Fragments: 29418047 total (28896044 tlen-paired, 3009 hash-paired, 249 singletons, 100669 discordant, 418076 orphans, 40249 too large [>5000 bp], 9327640 duplicates)