.command.out - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_SCORE (pos_somatic_022)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/b10da4e80642fbd33c22bf050a931f/.command.out
Size: 1.1 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_SCORE (pos_somatic_022)
Attempt

Content

[predict] Loading model from model.pkl …
  28 features loaded (LGBMClassifier, of 36 computed by annotator)
[predict] Loading PoN from pon …
  1D bins: 43,871  2D pairs: 39,238
[predict] Loading COSMIC from cosmic_fusion.tsv.gz …
  614 gene-pair orientations
[predict] Loading gene annotator from protein_coding_genes.bed …
[predict] Loading target panel from foresight_panel_for_manta.bed …
  201,779 panel intervals across 26 contigs
[predict] Tumor sample ID: 'FFPE_HD789_01_p1_gDNA_0005_A23NYHCLT4_1'  Normal sample ID: 'NA12878_c_0002_gDNA_0005_B23KYWJLT4_1'
[predict] Parsing VCF pos_somatic_022.manta_fusion.somatic_sv.annotated.vcf.gz …
  106 calls parsed (after intergenic/same-gene/on_panel filter)
  45 killed by hard filters → 61 surviving
  is_paralog_of_higher_score_call=1 for 0/61 calls
[predict] Scored 61 calls: 42 PASS at threshold 0.05
  After strict-match dedup: 49 calls (40 PASS)
  Final call set: 49 calls (40 PASS)
[predict] Writing pos_somatic_022.manta_fusion.somatic_sv.scored.vcf.gz …
[predict] Writing pos_somatic_022.manta_fusion.fusion_calls.tsv …
[predict] Done.