Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/02b2898dba79901df47bb2896274d8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_6SL-N1-BDNA-1_B23MHTGLT4_1/1136_6SL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  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/eb/02b2898dba79901df47bb2896274d8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_6SL-N1-BDNA-1_B23MHTGLT4_1/1136_6SL-N1-BDNA-1_B23MHTGLT4_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_6SL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6SL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6SL-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6SL-N1-BDNA-1_B23MHTGLT4_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: 88857374 total, 64153 skipped (flags/unmapped)
Fragments: 44660835 total (44092098 tlen-paired, 2992 hash-paired, 487 singletons, 15474 discordant, 549784 orphans, 10911 too large [>5000 bp], 16522469 duplicates)
Reads: 94135238 total, 56623 skipped (flags/unmapped)
Fragments: 47314194 total (46724850 tlen-paired, 3477 hash-paired, 518 singletons, 10188 discordant, 575161 orphans, 12953 too large [>5000 bp], 17147345 duplicates)
Reads: 102507039 total, 62697 skipped (flags/unmapped)
Fragments: 51528621 total (50846750 tlen-paired, 3289 hash-paired, 499 singletons, 15476 discordant, 662607 orphans, 25103 too large [>5000 bp], 19141965 duplicates)
Reads: 104728890 total, 104919 skipped (flags/unmapped)
Fragments: 52922406 total (51011882 tlen-paired, 3532 hash-paired, 498 singletons, 375847 discordant, 1530647 orphans, 155152 too large [>5000 bp], 19527734 duplicates)