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/1d/e0031281dc4d52592a278d01ffcc73/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/e0031281dc4d52592a278d01ffcc73/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-eb5d3959-7137-45a9-9f26-41f9201dcf7f/59/592956b79446ffc995a3a4164772d8/starfusion_filter_config.yaml Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/blacklist_breakpoint_database_2026-04-27.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/6fbf9d305c15bcccec495fa1104349/aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.tsv ==> STAGING COMPLETE (6 inputs) === DEBUGGING INFORMATION === Current working directory: /tmp/nxf.zaEDe4Uy9s Input files: - starfusion_tsv: aih-tih-sc-e1cae1-R1_A23YTGFLT4_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.zaEDe4Uy9s/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.zaEDe4Uy9s/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64736 drwx------. 3 1000 root 4096 Jun 8 08:49 . drwxrwxrwx. 4 root root 86 Jun 8 08:49 .. -rw-r--r--. 1 1000 root 0 Jun 8 08:49 .command.err -rw-r--r--. 1 1000 root 884 Jun 8 08:49 .command.out -rw-r--r--. 1 1000 root 14589 Jun 8 08:49 .command.run -rw-r--r--. 1 1000 root 3236 Jun 8 08:49 .command.sh -rw-r--r--. 1 1000 root 0 Jun 8 08:49 .command.trace -rw-r--r--. 1 1000 root 752277 Jun 8 08:49 aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 10714998 Jun 8 08:49 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 8 08:49 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 8 08:49 nextflow-bin -rw-r--r--. 1 1000 root 4128 Jun 8 08:49 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-e1cae1-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 2376 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 2376 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 170 of 2376 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 107 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: 3 pass (CALL=1), 2373 fail (CALL=0) Total fusions: 2376 (all rows retained) Added FILTER column: PASS=3, FAIL=2373 ✓ Verified: All 217 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 2376 Pass (CALL=1): 3 (0.1%) Fail (CALL=0): 2373 (99.9%) Blacklist Flagging: Total blacklisted: 217 ✓ All 217 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 1406 Excluded SpliceType: INCL_NON_REF_SPLICE: 657 Blacklisted: 110 Blacklisted; aih_curated_blacklist score(3): 59 Read count too low: 2 < 8: 48 aih_curated_blacklist score(3): 44 Excluded annotation pattern: HGNC_GENEFAM: 27 Read count too low: 3 < 8: 9 Excluded annotation pattern: DGD_PARALOGS: 6 aih_curated_blacklist score(5): 2 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 1 pass, 956 fail (total: 957) ONLY_REF_SPLICE: 2 pass, 1417 fail (total: 1419) Read Count Statistics: Fusions with < 3 total reads: 2310 Of these, 2310 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 2376 CALL=1 (pass): 3 CALL=0 (fail): 2373 ✓ Passing fusions (CALL=1) exported to: aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================