Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/2b755aa7f40cbedaaa4b9a42b88d38/.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/96/2b755aa7f40cbedaaa4b9a42b88d38/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_U4M-N1-BDNA-1_A23TY7KLT4_1/1241_U4M-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_U4M-N1-BDNA-1_A23TY7KLT4_1/1241_U4M-N1-BDNA-1_A23TY7KLT4_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_U4M-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_U4M-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_U4M-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_U4M-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: 80749310 total, 55218 skipped (flags/unmapped)
Fragments: 40446939 total (40217782 tlen-paired, 3258 hash-paired, 312 singletons, 10923 discordant, 214664 orphans, 7595 too large [>5000 bp], 13709749 duplicates)
Reads: 85964722 total, 49121 skipped (flags/unmapped)
Fragments: 43063626 total (42816799 tlen-paired, 5183 hash-paired, 280 singletons, 9543 discordant, 231821 orphans, 10225 too large [>5000 bp], 14691415 duplicates)
Reads: 86579705 total, 44415 skipped (flags/unmapped)
Fragments: 43370576 total (43137325 tlen-paired, 3521 hash-paired, 385 singletons, 7712 discordant, 221633 orphans, 8078 too large [>5000 bp], 14434496 duplicates)
Reads: 94264641 total, 80227 skipped (flags/unmapped)
Fragments: 47291796 total (46667571 tlen-paired, 2273 hash-paired, 363 singletons, 120316 discordant, 501273 orphans, 51229 too large [>5000 bp], 16177492 duplicates)