Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7J8-N1-BDNA-1_A23NMNVLT4_1/1136_7J8-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/74054180786a6fad1233659cb249ce/.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/08/74054180786a6fad1233659cb249ce/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7J8-N1-BDNA-1_A23NMNVLT4_1/1136_7J8-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> 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_7J8-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7J8-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7J8-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7J8-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: 52022351 total, 41146 skipped (flags/unmapped)
Fragments: 26055372 total (25905079 tlen-paired, 2259 hash-paired, 241 singletons, 7649 discordant, 140144 orphans, 5423 too large [>5000 bp], 6655169 duplicates)
Reads: 56120403 total, 32457 skipped (flags/unmapped)
Fragments: 28110806 total (27960934 tlen-paired, 1470 hash-paired, 261 singletons, 5084 discordant, 143057 orphans, 4826 too large [>5000 bp], 7073039 duplicates)
Reads: 62005319 total, 35703 skipped (flags/unmapped)
Fragments: 31058978 total (30890955 tlen-paired, 3010 hash-paired, 205 singletons, 7425 discordant, 157383 orphans, 4624 too large [>5000 bp], 8029480 duplicates)
Reads: 61907010 total, 57648 skipped (flags/unmapped)
Fragments: 31058094 total (30644698 tlen-paired, 2182 hash-paired, 246 singletons, 78270 discordant, 332698 orphans, 33059 too large [>5000 bp], 8036253 duplicates)