Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_7F2-N1-BDNA-1_A23TY7KLT4_1/1241_7F2-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/267ac6dcd7cd7539c310a9a541ea94/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_7F2-N1-BDNA-1_A23TY7KLT4_1/1241_7F2-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  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/52/267ac6dcd7cd7539c310a9a541ea94/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_7F2-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_7F2-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_7F2-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_7F2-N1-BDNA-1_A23TY7KLT4_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: 65998551 total, 48208 skipped (flags/unmapped)
Fragments: 33057277 total (32866178 tlen-paired, 3777 hash-paired, 257 singletons, 8747 discordant, 178318 orphans, 7182 too large [>5000 bp], 10606568 duplicates)
Reads: 70806265 total, 38644 skipped (flags/unmapped)
Fragments: 35468486 total (35276752 tlen-paired, 2242 hash-paired, 355 singletons, 6137 discordant, 183000 orphans, 7002 too large [>5000 bp], 11166790 duplicates)
Reads: 77563865 total, 69993 skipped (flags/unmapped)
Fragments: 38918408 total (38385832 tlen-paired, 2879 hash-paired, 306 singletons, 100977 discordant, 428414 orphans, 42888 too large [>5000 bp], 12544219 duplicates)
Reads: 77152886 total, 44134 skipped (flags/unmapped)
Fragments: 38653112 total (38416398 tlen-paired, 4376 hash-paired, 263 singletons, 8892 discordant, 223183 orphans, 12987 too large [>5000 bp], 12441865 duplicates)