Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BWD8-N1-BDNA-1_A23TNVNLT4_1/1241_BWD8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BWD8-N1-BDNA-1_A23TNVNLT4_1/1241_BWD8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/bb6c1802dcce8bb5cc29d67bde4a9e/.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/4e/bb6c1802dcce8bb5cc29d67bde4a9e/.command.run
==> STAGING COMPLETE (5 inputs)

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: 1241_BWD8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_BWD8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_BWD8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BWD8-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 38581075 total, 44044 skipped (flags/unmapped)
Fragments: 19740851 total (18778384 tlen-paired, 2961 hash-paired, 221 singletons, 3533 discordant, 955752 orphans, 5651 too large [>5000 bp], 9743417 duplicates)
Reads: 40871601 total, 41146 skipped (flags/unmapped)
Fragments: 20960591 total (19849969 tlen-paired, 2047 hash-paired, 318 singletons, 2596 discordant, 1105661 orphans, 7626 too large [>5000 bp], 10112384 duplicates)
Reads: 41590586 total, 39270 skipped (flags/unmapped)
Fragments: 21301199 total (20223528 tlen-paired, 2260 hash-paired, 162 singletons, 3237 discordant, 1072012 orphans, 10546 too large [>5000 bp], 10683962 duplicates)
Reads: 50230884 total, 90026 skipped (flags/unmapped)
Fragments: 26287175 total (22379944 tlen-paired, 2552 hash-paired, 379 singletons, 826769 discordant, 3077531 orphans, 322209 too large [>5000 bp], 12324941 duplicates)