Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/869_TE4-N1-BDNA-1_B23T7FYLT4_1/869_TE4-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/a565c84f5de832a1639249c776826e/.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/ae/a565c84f5de832a1639249c776826e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/869_TE4-N1-BDNA-1_B23T7FYLT4_1/869_TE4-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_TE4-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.baiThe index file is older than the data file: 869_TE4-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_TE4-N1-BDNA-1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_TE4-N1-BDNA-1_B23T7FYLT4_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: 408019152 total, 311865 skipped (flags/unmapped)
Fragments: 204803881 total (202763661 tlen-paired, 18647 hash-paired, 2115 singletons, 41756 discordant, 1977702 orphans, 39671 too large [>5000 bp], 113939044 duplicates)
Reads: 449769983 total, 247226 skipped (flags/unmapped)
Fragments: 225867907 total (223521304 tlen-paired, 15616 hash-paired, 2957 singletons, 29428 discordant, 2298602 orphans, 44251 too large [>5000 bp], 125211475 duplicates)
Reads: 484829951 total, 285990 skipped (flags/unmapped)
Fragments: 243425582 total (240831113 tlen-paired, 41896 hash-paired, 2505 singletons, 43230 discordant, 2506838 orphans, 101070 too large [>5000 bp], 136060949 duplicates)
Reads: 494358324 total, 560439 skipped (flags/unmapped)
Fragments: 249323605 total (241759096 tlen-paired, 21595 hash-paired, 2895 singletons, 1530791 discordant, 6009228 orphans, 581399 too large [>5000 bp], 138383129 duplicates)