File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/ac606e02b66e21523e29eb1e02ef7e/.command.log
Size
2.7 KB
Task
SOMATIC_CNV_REF_BUILDER:SOMA_CNV_PROBE_COUNTS (869_I3-N1-BDNA-1_A23H3NYLT3_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/ac606e02b66e21523e29eb1e02ef7e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_I3-N1-BDNA-1_A23H3NYLT3_1/869_I3-N1-BDNA-1_A23H3NYLT3_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/6e/ac606e02b66e21523e29eb1e02ef7e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_I3-N1-BDNA-1_A23H3NYLT3_1/869_I3-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
==> 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: 869_I3-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_I3-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_I3-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_I3-N1-BDNA-1_A23H3NYLT3_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: 75884422 total, 67897 skipped (flags/unmapped)
Fragments: 38090392 total (37685869 tlen-paired, 14976 hash-paired, 7425 singletons, 6782 discordant, 375340 orphans, 9253 too large [>5000 bp], 4986773 duplicates)
Reads: 81949222 total, 57631 skipped (flags/unmapped)
Fragments: 41156279 total (40693996 tlen-paired, 15799 hash-paired, 7774 singletons, 5511 discordant, 433199 orphans, 10003 too large [>5000 bp], 5348117 duplicates)
Reads: 82034386 total, 59474 skipped (flags/unmapped)
Fragments: 41193317 total (40735358 tlen-paired, 13357 hash-paired, 7684 singletons, 7038 discordant, 429880 orphans, 12921 too large [>5000 bp], 5360225 duplicates)
Reads: 83546034 total, 106504 skipped (flags/unmapped)
Fragments: 42175449 total (40768279 tlen-paired, 13255 hash-paired, 7864 singletons, 273409 discordant, 1112642 orphans, 104569 too large [>5000 bp], 5405873 duplicates)