Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/f73194e1ccb38a76b939810b749aa2/BT-20_FFPE_RNA_0001_B23LG7FLT4_3.starfusion.starfusion.fusion_predictions.tsv Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/a7ff4913eed814dfe7252b5c076419/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/a7ff4913eed814dfe7252b5c076419/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/58/2f66683c63e8e0a2b7a3c46113f09d/starfusion_filter_config.yaml Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/blacklist_breakpoint_database_2026-04-27.tsv ==> STAGING COMPLETE (6 inputs) === DEBUGGING INFORMATION === Current working directory: /tmp/nxf.52qOjMfYhB Input files: - starfusion_tsv: BT-20_FFPE_RNA_0001_B23LG7FLT4_3.starfusion.starfusion.fusion_predictions.tsv - blacklist: blacklist_hg38_GRCh38_v2.4.0.tsv.gz - filter_config: starfusion_filter_config.yaml - aih_blacklist_breakpoints: blacklist_breakpoint_database_2026-04-27.tsv === PYTHON INFORMATION === /usr/local/bin/python Python 3.11.14 /usr/local/bin/python3 Python 3.11.14 === SCRIPT LOCATION === Checking for filter_starfusion_main.py: /tmp/nxf.52qOjMfYhB/nextflow-bin/filter_starfusion_main.py filter_starfusion_main.py not in current directory bin/filter_starfusion_main.py not found bin/ directory does not exist === ENVIRONMENT PATH === /tmp/nxf.52qOjMfYhB/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64300 drwx------. 3 1000 root 4096 Jun 8 08:16 . drwxrwxrwx. 4 root root 86 Jun 8 08:16 .. -rw-r--r--. 1 1000 root 0 Jun 8 08:16 .command.err -rw-r--r--. 1 1000 root 883 Jun 8 08:16 .command.out -rw-r--r--. 1 1000 root 14585 Jun 8 08:16 .command.run -rw-r--r--. 1 1000 root 3230 Jun 8 08:16 .command.sh -rw-r--r--. 1 1000 root 0 Jun 8 08:16 .command.trace -rw-r--r--. 1 1000 root 305758 Jun 8 08:16 BT-20_FFPE_RNA_0001_B23LG7FLT4_3.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 10714998 Jun 8 08:16 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 8 08:16 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 8 08:16 nextflow-bin -rw-r--r--. 1 1000 root 4128 Jun 8 08:16 starfusion_filter_config.yaml === PROJECT DIRECTORY INFO === NXF_PROJECT_DIR: not set baseDir: not set === Running filter script === ================================================================================ STEP 1: LOADING STAR-FUSION PREDICTIONS ================================================================================ Loading STAR-Fusion predictions from: BT-20_FFPE_RNA_0001_B23LG7FLT4_3.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 1035 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 1035 valid, 0 invalid ================================================================================ STEP 3: FLAGGING WITH BLACKLIST ================================================================================ Loading blacklist (this may take a while)... Loading blacklist from: blacklist_hg38_GRCh38_v2.4.0.tsv.gz Loaded 9381 single rules and 16721785 pair rules Indexed blacklist (bin_size=100000) Flagging fusions with blacklist... ✓ Flagged 64 of 1035 fusions as blacklisted ================================================================================ STEP 3b: AIH CURATED BREAKPOINT BLACKLIST ================================================================================ Loading AIH blacklist table from: blacklist_breakpoint_database_2026-04-27.tsv Qualified breakpoint keys (orientations): 1378 AIH curated blacklist: matched 66 fusion rows (breakpoint_ID in qualified set) ================================================================================ STEP 4: APPLYING YAML-BASED FILTER ================================================================================ ✓ Filter initialized from: starfusion_filter_config.yaml Applying filter criteria (adding CALL column)... ✓ Filter applied: 0 pass (CALL=1), 1035 fail (CALL=0) Total fusions: 1035 (all rows retained) Added FILTER column: PASS=0, FAIL=1035 ✓ Verified: All 106 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 1035 Pass (CALL=1): 0 (0.0%) Fail (CALL=0): 1035 (100.0%) Blacklist Flagging: Total blacklisted: 106 ✓ All 106 blacklisted fusions have CALL=0 Failure Reasons (top 10): Excluded SpliceType: INCL_NON_REF_SPLICE: 615 Read count too low: 1 < 8: 270 Blacklisted: 40 aih_curated_blacklist score(3): 38 Excluded annotation pattern: HGNC_GENEFAM: 26 Blacklisted; aih_curated_blacklist score(3): 24 Read count too low: 2 < 8: 11 Read count too low: 3 < 8: 3 aih_curated_blacklist score(5): 3 Excluded annotation pattern: GTEx_recurrent_StarF2019: 3 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 0 pass, 768 fail (total: 768) ONLY_REF_SPLICE: 0 pass, 267 fail (total: 267) Read Count Statistics: Fusions with < 3 total reads: 1014 Of these, 1014 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: BT-20_FFPE_RNA_0001_B23LG7FLT4_3.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 1035 CALL=1 (pass): 0 CALL=0 (fail): 1035 ✓ Empty pass_only file created (no passing fusions): BT-20_FFPE_RNA_0001_B23LG7FLT4_3.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: BT-20_FFPE_RNA_0001_B23LG7FLT4_3.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================