File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/6ca2c4635785637a8d4be34879fe16/.command.log
Size
2.4 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_PROBE_COUNTS (HCC1395_tumor)
Attempt

Content

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  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/6ca2c4635785637a8d4be34879fe16/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/6ca2c4635785637a8d4be34879fe16/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/bed/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_chr21.bed
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Reads: 6171 total, 429 skipped (flags/unmapped)
Fragments: 2961 total (2776 tlen-paired, 0 hash-paired, 0 singletons, 5 discordant, 180 orphans, 0 too large [>5000 bp], 147 duplicates)
Reads: 10265 total, 1265 skipped (flags/unmapped)
Fragments: 4573 total (4420 tlen-paired, 4 hash-paired, 0 singletons, 1 discordant, 148 orphans, 1 too large [>5000 bp], 352 duplicates)
Reads: 8903 total, 566 skipped (flags/unmapped)
Fragments: 4224 total (4112 tlen-paired, 0 hash-paired, 0 singletons, 1 discordant, 111 orphans, 0 too large [>5000 bp], 320 duplicates)
Reads: 5256004 total, 2965 skipped (flags/unmapped)
Fragments: 2626071 total (2624186 tlen-paired, 930 hash-paired, 34 singletons, 110 discordant, 811 orphans, 871 too large [>5000 bp], 1037682 duplicates)