Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_6IX-N1-BDNA-1_A23NMNVLT4_1/1136_6IX-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_6IX-N1-BDNA-1_A23NMNVLT4_1/1136_6IX-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/315c4f096069305f008d7b483f25ed/.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/09/315c4f096069305f008d7b483f25ed/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_6IX-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_6IX-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_6IX-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6IX-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: 53756692 total, 42346 skipped (flags/unmapped)
Fragments: 26980658 total (26712701 tlen-paired, 2529 hash-paired, 227 singletons, 4984 discordant, 260217 orphans, 6737 too large [>5000 bp], 7567535 duplicates)
Reads: 63378031 total, 38193 skipped (flags/unmapped)
Fragments: 31819387 total (31485739 tlen-paired, 1894 hash-paired, 229 singletons, 4942 discordant, 326583 orphans, 13938 too large [>5000 bp], 8984207 duplicates)
Reads: 64612808 total, 65345 skipped (flags/unmapped)
Fragments: 32580172 total (31608214 tlen-paired, 2293 hash-paired, 387 singletons, 195794 discordant, 773484 orphans, 80495 too large [>5000 bp], 9120423 duplicates)
Reads: 57509254 total, 35527 skipped (flags/unmapped)
Fragments: 28871568 total (28586025 tlen-paired, 1706 hash-paired, 276 singletons, 3620 discordant, 279941 orphans, 5404 too large [>5000 bp], 7895501 duplicates)