Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/303e65f164623fb84ebcd4ad16f92d/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_eNS-N1-BDNA-1_B23MHTGLT4_1/659_eNS-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_eNS-N1-BDNA-1_B23MHTGLT4_1/659_eNS-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  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/2a/303e65f164623fb84ebcd4ad16f92d/.command.run
==> 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: 659_eNS-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_eNS-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eNS-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eNS-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: 81419492 total, 60889 skipped (flags/unmapped)
Fragments: 40883717 total (40438804 tlen-paired, 3438 hash-paired, 426 singletons, 13894 discordant, 427155 orphans, 9375 too large [>5000 bp], 12458831 duplicates)
Reads: 87419735 total, 52962 skipped (flags/unmapped)
Fragments: 43898834 total (43436651 tlen-paired, 3274 hash-paired, 471 singletons, 10126 discordant, 448312 orphans, 8944 too large [>5000 bp], 13132871 duplicates)
Reads: 85989694 total, 56372 skipped (flags/unmapped)
Fragments: 43186410 total (42699098 tlen-paired, 4030 hash-paired, 371 singletons, 12116 discordant, 470795 orphans, 15834 too large [>5000 bp], 13260488 duplicates)
Reads: 95638880 total, 94464 skipped (flags/unmapped)
Fragments: 48218298 total (46804570 tlen-paired, 3706 hash-paired, 440 singletons, 282208 discordant, 1127374 orphans, 117817 too large [>5000 bp], 14771954 duplicates)