Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/6d19f3ab13d28b05abdb0181c9cd69/aih-tih-sc-560d56-R1_A23WJ53LT4_1.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/87/8c1ea4f532c6de9a1c4bb45b4c1d13/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/8c1ea4f532c6de9a1c4bb45b4c1d13/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/e2/67df0cc053219f9b526f729943f15d/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.GFIit0ODUe Input files: - starfusion_tsv: aih-tih-sc-560d56-R1_A23WJ53LT4_1.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.GFIit0ODUe/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.GFIit0ODUe/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64524 drwx------. 3 1000 root 4096 Jun 8 08:57 . drwxrwxrwx. 4 root root 86 Jun 8 08:57 .. -rw-r--r--. 1 1000 root 0 Jun 8 08:57 .command.err -rw-r--r--. 1 1000 root 884 Jun 8 08:57 .command.out -rw-r--r--. 1 1000 root 14589 Jun 8 08:57 .command.run -rw-r--r--. 1 1000 root 3236 Jun 8 08:57 .command.sh -rw-r--r--. 1 1000 root 0 Jun 8 08:57 .command.trace -rw-r--r--. 1 1000 root 533246 Jun 8 08:57 aih-tih-sc-560d56-R1_A23WJ53LT4_1.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 10714998 Jun 8 08:57 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 8 08:57 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 8 08:57 nextflow-bin -rw-r--r--. 1 1000 root 4128 Jun 8 08:57 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: aih-tih-sc-560d56-R1_A23WJ53LT4_1.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 1693 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 1693 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 139 of 1693 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 84 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: 5 pass (CALL=1), 1688 fail (CALL=0) Total fusions: 1693 (all rows retained) Added FILTER column: PASS=5, FAIL=1688 ✓ Verified: All 175 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 1693 Pass (CALL=1): 5 (0.3%) Fail (CALL=0): 1688 (99.7%) Blacklist Flagging: Total blacklisted: 175 ✓ All 175 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 814 Excluded SpliceType: INCL_NON_REF_SPLICE: 607 Blacklisted: 91 Read count too low: 2 < 8: 52 Blacklisted; aih_curated_blacklist score(3): 48 aih_curated_blacklist score(3): 34 Excluded annotation pattern: HGNC_GENEFAM: 24 Read count too low: 3 < 8: 8 Excluded annotation pattern: GTEx_recurrent_StarF2019: 4 Read count too low: 4 < 8: 2 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 1 pass, 841 fail (total: 842) ONLY_REF_SPLICE: 4 pass, 847 fail (total: 851) Read Count Statistics: Fusions with < 3 total reads: 1631 Of these, 1631 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: aih-tih-sc-560d56-R1_A23WJ53LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 1693 CALL=1 (pass): 5 CALL=0 (fail): 1688 ✓ Passing fusions (CALL=1) exported to: aih-tih-sc-560d56-R1_A23WJ53LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: aih-tih-sc-560d56-R1_A23WJ53LT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================