Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_5Z8-N1-BDNA-1_A23TY7KLT4_1/1241_5Z8-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_5Z8-N1-BDNA-1_A23TY7KLT4_1/1241_5Z8-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/540b07cf0c4d9d012ac9f17dbeab7f/.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/12/540b07cf0c4d9d012ac9f17dbeab7f/.command.run
==> 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_5Z8-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_5Z8-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_5Z8-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_5Z8-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: 90760239 total, 65659 skipped (flags/unmapped)
Fragments: 45470555 total (45184703 tlen-paired, 2803 hash-paired, 426 singletons, 15657 discordant, 266966 orphans, 10431 too large [>5000 bp], 16427125 duplicates)
Reads: 97671109 total, 57586 skipped (flags/unmapped)
Fragments: 48932086 total (48642885 tlen-paired, 3964 hash-paired, 451 singletons, 10554 discordant, 274232 orphans, 12017 too large [>5000 bp], 17477301 duplicates)
Reads: 106502088 total, 92489 skipped (flags/unmapped)
Fragments: 53454285 total (52692904 tlen-paired, 2177 hash-paired, 392 singletons, 142817 discordant, 615995 orphans, 58708 too large [>5000 bp], 19507764 duplicates)
Reads: 106094405 total, 61429 skipped (flags/unmapped)
Fragments: 53157516 total (52821554 tlen-paired, 7382 hash-paired, 336 singletons, 15112 discordant, 313132 orphans, 15706 too large [>5000 bp], 19394451 duplicates)