Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_V8X-N1-BDNA-1_B23MHTGLT4_1/1029_V8X-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/a0719ec0cf33d4a71e2b628505d496/.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/e3/a0719ec0cf33d4a71e2b628505d496/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_V8X-N1-BDNA-1_B23MHTGLT4_1/1029_V8X-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: 1029_V8X-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1029_V8X-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_V8X-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_V8X-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: 70509709 total, 51262 skipped (flags/unmapped)
Fragments: 35404464 total (35018162 tlen-paired, 2872 hash-paired, 402 singletons, 12199 discordant, 370829 orphans, 10375 too large [>5000 bp], 10691044 duplicates)
Reads: 74997568 total, 41257 skipped (flags/unmapped)
Fragments: 37660130 total (37268501 tlen-paired, 2721 hash-paired, 487 singletons, 8403 discordant, 380018 orphans, 8278 too large [>5000 bp], 11200983 duplicates)
Reads: 81675853 total, 46577 skipped (flags/unmapped)
Fragments: 41019027 total (40567277 tlen-paired, 3310 hash-paired, 376 singletons, 12484 discordant, 435580 orphans, 13589 too large [>5000 bp], 12476630 duplicates)
Reads: 82647173 total, 77080 skipped (flags/unmapped)
Fragments: 41678671 total (40447389 tlen-paired, 2798 hash-paired, 435 singletons, 239311 discordant, 988738 orphans, 100962 too large [>5000 bp], 12670114 duplicates)