Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7LE-N1-BDNA-1_A23NMNVLT4_1/1136_7LE-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_7LE-N1-BDNA-1_A23NMNVLT4_1/1136_7LE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/da6864e9e9e7b0675e3151e28fc428/.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/87/da6864e9e9e7b0675e3151e28fc428/.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_7LE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7LE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7LE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7LE-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: 42718561 total, 24209 skipped (flags/unmapped)
Fragments: 21395890 total (21285309 tlen-paired, 1369 hash-paired, 153 singletons, 3676 discordant, 105383 orphans, 4054 too large [>5000 bp], 5768232 duplicates)
Reads: 39830237 total, 28874 skipped (flags/unmapped)
Fragments: 19949492 total (19837487 tlen-paired, 1343 hash-paired, 178 singletons, 5911 discordant, 104573 orphans, 3565 too large [>5000 bp], 5482409 duplicates)
Reads: 47431767 total, 41942 skipped (flags/unmapped)
Fragments: 23793675 total (23489279 tlen-paired, 1301 hash-paired, 182 singletons, 57212 discordant, 245701 orphans, 24179 too large [>5000 bp], 6572411 duplicates)
Reads: 47357986 total, 26997 skipped (flags/unmapped)
Fragments: 23722391 total (23587798 tlen-paired, 1848 hash-paired, 172 singletons, 5738 discordant, 126835 orphans, 6607 too large [>5000 bp], 6531434 duplicates)