Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0K5-N1-BDNA-1_A23MHW3LT4_1/1136_0K5-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/119c79e087ea4fe582a23e40f499b4/.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/0f/119c79e087ea4fe582a23e40f499b4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0K5-N1-BDNA-1_A23MHW3LT4_1/1136_0K5-N1-BDNA-1_A23MHW3LT4_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_0K5-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0K5-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0K5-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0K5-N1-BDNA-1_A23MHW3LT4_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: 30432685 total, 44821 skipped (flags/unmapped)
Fragments: 15671909 total (14700653 tlen-paired, 3542 hash-paired, 262 singletons, 2846 discordant, 964606 orphans, 4457 too large [>5000 bp], 6760362 duplicates)
Reads: 31616294 total, 47054 skipped (flags/unmapped)
Fragments: 16282948 total (15270281 tlen-paired, 3172 hash-paired, 348 singletons, 2285 discordant, 1006862 orphans, 5277 too large [>5000 bp], 6836181 duplicates)
Reads: 35005751 total, 46937 skipped (flags/unmapped)
Fragments: 18028887 total (16903550 tlen-paired, 5939 hash-paired, 253 singletons, 3198 discordant, 1115947 orphans, 8620 too large [>5000 bp], 7765095 duplicates)
Reads: 39008149 total, 71764 skipped (flags/unmapped)
Fragments: 20664213 total (16852168 tlen-paired, 2913 hash-paired, 427 singletons, 771135 discordant, 3037570 orphans, 322978 too large [>5000 bp], 8207956 duplicates)