Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_0R8-N1-BDNA-1_A23TNVNLT4_1/1241_0R8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/39b6ef7e41cdb9331b885b96eb5ae2/.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/e1/39b6ef7e41cdb9331b885b96eb5ae2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_0R8-N1-BDNA-1_A23TNVNLT4_1/1241_0R8-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_0R8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_0R8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_0R8-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_0R8-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: 87255967 total, 60708 skipped (flags/unmapped)
Fragments: 43760646 total (43396855 tlen-paired, 3864 hash-paired, 478 singletons, 14128 discordant, 345321 orphans, 9883 too large [>5000 bp], 16673248 duplicates)
Reads: 93442405 total, 51238 skipped (flags/unmapped)
Fragments: 46869575 total (46489320 tlen-paired, 3009 hash-paired, 549 singletons, 10105 discordant, 366592 orphans, 9579 too large [>5000 bp], 17500531 duplicates)
Reads: 103385581 total, 54863 skipped (flags/unmapped)
Fragments: 51858496 total (51404154 tlen-paired, 6846 hash-paired, 385 singletons, 15908 discordant, 431203 orphans, 22657 too large [>5000 bp], 19933035 duplicates)
Reads: 105372481 total, 98273 skipped (flags/unmapped)
Fragments: 52997688 total (51868818 tlen-paired, 3269 hash-paired, 454 singletons, 223259 discordant, 901888 orphans, 90587 too large [>5000 bp], 20318418 duplicates)