Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_7RV-N1-BDNA-1_B23MHTGLT4_1/1136_7RV-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/81c05a7988b189e554adee1f5b4a95/.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/de/81c05a7988b189e554adee1f5b4a95/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_7RV-N1-BDNA-1_B23MHTGLT4_1/1136_7RV-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_7RV-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7RV-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7RV-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7RV-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: 75638499 total, 54933 skipped (flags/unmapped)
Fragments: 37980848 total (37564020 tlen-paired, 2755 hash-paired, 427 singletons, 13545 discordant, 400101 orphans, 11199 too large [>5000 bp], 11915275 duplicates)
Reads: 88907878 total, 88014 skipped (flags/unmapped)
Fragments: 44820936 total (43514244 tlen-paired, 3973 hash-paired, 488 singletons, 262181 discordant, 1040050 orphans, 109265 too large [>5000 bp], 14087771 duplicates)
Reads: 80656369 total, 49036 skipped (flags/unmapped)
Fragments: 40499451 total (40074935 tlen-paired, 2846 hash-paired, 515 singletons, 9011 discordant, 412144 orphans, 10545 too large [>5000 bp], 12391027 duplicates)
Reads: 79883477 total, 50470 skipped (flags/unmapped)
Fragments: 40120576 total (39652884 tlen-paired, 4298 hash-paired, 428 singletons, 11959 discordant, 451007 orphans, 21645 too large [>5000 bp], 12651399 duplicates)