Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_I-N1-BDNA-1_A23NMNVLT4_1/1029_I-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/d161c7c80b2aaebc0b000dc66fba5d/.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/99/d161c7c80b2aaebc0b000dc66fba5d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_I-N1-BDNA-1_A23NMNVLT4_1/1029_I-N1-BDNA-1_A23NMNVLT4_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: 1029_I-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I-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: 65566052 total, 58179 skipped (flags/unmapped)
Fragments: 32842116 total (32633806 tlen-paired, 3213 hash-paired, 319 singletons, 11856 discordant, 192922 orphans, 8441 too large [>5000 bp], 9412152 duplicates)
Reads: 71196033 total, 45546 skipped (flags/unmapped)
Fragments: 35666915 total (35457534 tlen-paired, 3085 hash-paired, 369 singletons, 8053 discordant, 197874 orphans, 7450 too large [>5000 bp], 9992058 duplicates)
Reads: 70989416 total, 51536 skipped (flags/unmapped)
Fragments: 35564511 total (35330549 tlen-paired, 2236 hash-paired, 290 singletons, 9916 discordant, 221520 orphans, 15334 too large [>5000 bp], 10287390 duplicates)
Reads: 78259638 total, 81883 skipped (flags/unmapped)
Fragments: 39261017 total (38724259 tlen-paired, 2523 hash-paired, 366 singletons, 103098 discordant, 430771 orphans, 43429 too large [>5000 bp], 11361169 duplicates)