File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4adc35c57b0fe7180506cfa8c8f523/.command.log
Size
2.3 KB
Task
MIX_BAMS (HG00741_x_HG01106_FF_5)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4adc35c57b0fe7180506cfa8c8f523/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20260210_LH00519_0056_A23K2N2LT4/1076-add-custom-fastq-sample-merging_afd6c9_260212144006/bams/3599996073_r8_L37.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20251024_LH00519_0040_A235HV2LT4/dev-renasight_eb7639_251029121806/bams/3567293746_r4.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20251024_LH00519_0040_A235HV2LT4/dev-renasight_eb7639_251029121806/bams/3567293746_r4.bam
  Downloading: s3://natera-platform-sandbox/projects/lcvs/bed-files/xgen-exome-research-panel-v2-targets-hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4adc35c57b0fe7180506cfa8c8f523/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20260210_LH00519_0056_A23K2N2LT4/1076-add-custom-fastq-sample-merging_afd6c9_260212144006/bams/3599996073_r8_L37.bam
==> STAGING COMPLETE (7 inputs)

[MIX_BAMS:HG00741_x_HG01106_FF_5] BED: 197769 intervals, sampled 2019 covering 359155 bp
[W::hts_idx_load3] The index file is older than the data file: 3567293746_r4.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 3599996073_r8_L37.bam.bai
[MIX_BAMS:HG00741_x_HG01106_FF_5] maternal: 3567293746_r4.bam reads=169452500 on_target_cov=223.9566x
[MIX_BAMS:HG00741_x_HG01106_FF_5] fetal:    3599996073_r8_L37.bam reads=154002685 on_target_cov=175.5632x
[MIX_BAMS:HG00741_x_HG01106_FF_5] effective target=200.0000x  fractions: mat=0.8484 fet=0.0570  status=OK
[MIX_BAMS:HG00741_x_HG01106_FF_5] after subsample: mat=143758199/169452500 fet=8779468/154002685
[bam_translate] PG tag "MarkDuplicates" on read "LH00519:40:235HV2LT4:1:2166:28522:2695" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "LH00519:56:23K2N2LT4:7:1197:13009:2177" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[MIX_BAMS:HG00741_x_HG01106_FF_5] mixture:  HG00741_x_HG01106_FF_5.mix.bam reads=152537667 on_target_cov=199.6495x observed_ff=0.0576