Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/df61fdcca81665123ed1c42a9fbb9e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_4BR-N1-BDNA-1_A23NMNVLT4_1/1029_4BR-N1-BDNA-1_A23NMNVLT4_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/fd/df61fdcca81665123ed1c42a9fbb9e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_4BR-N1-BDNA-1_A23NMNVLT4_1/1029_4BR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_4BR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_4BR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_4BR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_4BR-N1-BDNA-1_A23NMNVLT4_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: 87560487 total, 43589 skipped (flags/unmapped)
Fragments: 43867598 total (43621274 tlen-paired, 2592 hash-paired, 407 singletons, 9244 discordant, 234081 orphans, 8095 too large [>5000 bp], 10411909 duplicates)
Reads: 80255885 total, 50278 skipped (flags/unmapped)
Fragments: 40206940 total (39964773 tlen-paired, 2636 hash-paired, 358 singletons, 12242 discordant, 226931 orphans, 9508 too large [>5000 bp], 9724494 duplicates)
Reads: 86542979 total, 44888 skipped (flags/unmapped)
Fragments: 43364659 total (43082042 tlen-paired, 5501 hash-paired, 296 singletons, 11123 discordant, 265697 orphans, 17383 too large [>5000 bp], 10662247 duplicates)
Reads: 95414558 total, 75467 skipped (flags/unmapped)
Fragments: 47878180 total (47228215 tlen-paired, 3465 hash-paired, 344 singletons, 126161 discordant, 519995 orphans, 51535 too large [>5000 bp], 11804076 duplicates)