Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1047_CL-N1-BDNA-1_A23NMNVLT4_1/1047_CL-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/99e2caf7207899afa77410ea2f91a8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1047_CL-N1-BDNA-1_A23NMNVLT4_1/1047_CL-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  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/32/99e2caf7207899afa77410ea2f91a8/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_CL-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: 1047_CL-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1047_CL-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_CL-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 88308142 total, 66132 skipped (flags/unmapped)
Fragments: 44233184 total (43976346 tlen-paired, 2582 hash-paired, 409 singletons, 11664 discordant, 242183 orphans, 9117 too large [>5000 bp], 14740206 duplicates)
Reads: 94995183 total, 55030 skipped (flags/unmapped)
Fragments: 47587378 total (47325115 tlen-paired, 2640 hash-paired, 445 singletons, 7878 discordant, 251300 orphans, 8571 too large [>5000 bp], 15594956 duplicates)
Reads: 95103062 total, 61029 skipped (flags/unmapped)
Fragments: 47645835 total (47337439 tlen-paired, 6740 hash-paired, 347 singletons, 10497 discordant, 290812 orphans, 20761 too large [>5000 bp], 16017260 duplicates)
Reads: 105508182 total, 97594 skipped (flags/unmapped)
Fragments: 52936446 total (52208389 tlen-paired, 2984 hash-paired, 424 singletons, 143347 discordant, 581302 orphans, 59711 too large [>5000 bp], 17816888 duplicates)