Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/foresight_panel_for_manta.bed
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/b10da4e80642fbd33c22bf050a931f/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/protein_coding_genes.bed
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/7bf3d915a57f54d5501bfd601f256f/pos_somatic_022.manta_fusion.somatic_sv.annotated.vcf.gz.tbi
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/modelD/model.pkl
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/b10da4e80642fbd33c22bf050a931f/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/cosmic_fusion.tsv.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/7bf3d915a57f54d5501bfd601f256f/pos_somatic_022.manta_fusion.somatic_sv.annotated.vcf.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/pon
==> STAGING COMPLETE (9 inputs)
/usr/local/lib/python3.11/site-packages/sklearn/utils/validation.py:2691: UserWarning: X does not have valid feature names, but LGBMClassifier was fitted with feature names
warnings.warn(
[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.