Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_DI1-N1-BDNA-1_A23TNVNLT4_1/1241_DI1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/3023c3142202ed09fdbde2ca79932c/.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/99/3023c3142202ed09fdbde2ca79932c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_DI1-N1-BDNA-1_A23TNVNLT4_1/1241_DI1-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] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_DI1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_DI1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

The index file is older than the data file: 1241_DI1-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_DI1-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: 67558165 total, 47997 skipped (flags/unmapped)
Fragments: 33904823 total (33572125 tlen-paired, 2944 hash-paired, 377 singletons, 11498 discordant, 317879 orphans, 9389 too large [>5000 bp], 13073572 duplicates)
Reads: 72508598 total, 40538 skipped (flags/unmapped)
Fragments: 36397611 total (36044292 tlen-paired, 1943 hash-paired, 377 singletons, 8308 discordant, 342691 orphans, 7953 too large [>5000 bp], 13725962 duplicates)
Reads: 79117112 total, 42962 skipped (flags/unmapped)
Fragments: 39715584 total (39322304 tlen-paired, 3426 hash-paired, 302 singletons, 11516 discordant, 378036 orphans, 10660 too large [>5000 bp], 15344801 duplicates)
Reads: 80518130 total, 79477 skipped (flags/unmapped)
Fragments: 40567957 total (39490862 tlen-paired, 1870 hash-paired, 352 singletons, 212860 discordant, 862013 orphans, 82552 too large [>5000 bp], 15602568 duplicates)