Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_62L-N1-BDNA-1_A23NMNVLT4_1/1136_62L-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_62L-N1-BDNA-1_A23NMNVLT4_1/1136_62L-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/616840f1a63e7cd04c29a1d6ba240e/.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/d3/616840f1a63e7cd04c29a1d6ba240e/.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: 1136_62L-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_62L-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_62L-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_62L-N1-BDNA-1_A23NMNVLT4_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: 77118245 total, 45722 skipped (flags/unmapped)
Fragments: 38640555 total (38407973 tlen-paired, 2441 hash-paired, 405 singletons, 6794 discordant, 222942 orphans, 7380 too large [>5000 bp], 11655929 duplicates)
Reads: 71336347 total, 56426 skipped (flags/unmapped)
Fragments: 35740766 total (35510895 tlen-paired, 3559 hash-paired, 287 singletons, 10371 discordant, 215654 orphans, 7165 too large [>5000 bp], 10967101 duplicates)
Reads: 85292991 total, 85991 skipped (flags/unmapped)
Fragments: 42818011 total (42155367 tlen-paired, 1887 hash-paired, 359 singletons, 127233 discordant, 533165 orphans, 52251 too large [>5000 bp], 13298480 duplicates)
Reads: 84789619 total, 51279 skipped (flags/unmapped)
Fragments: 42487885 total (42198928 tlen-paired, 3712 hash-paired, 317 singletons, 10711 discordant, 274217 orphans, 18552 too large [>5000 bp], 13197222 duplicates)