Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/15f9976d174fd496e1b25f1ee599e6/aih-tih-sc-242a7d-R1_A23YTGFLT4_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/6b/d69e06f9b7f3fa86968b562dad7617/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/d69e06f9b7f3fa86968b562dad7617/.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 ==> STAGING COMPLETE (6 inputs) === DEBUGGING INFORMATION === Current working directory: /tmp/nxf.Kk2jhJayAT Input files: - starfusion_tsv: aih-tih-sc-242a7d-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.Kk2jhJayAT/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.Kk2jhJayAT/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64660 drwx------. 3 1000 root 4096 Jun 8 09:44 . drwxrwxrwx. 4 root root 86 Jun 8 09:44 .. -rw-r--r--. 1 1000 root 0 Jun 8 09:44 .command.err -rw-r--r--. 1 1000 root 884 Jun 8 09:44 .command.out -rw-r--r--. 1 1000 root 14589 Jun 8 09:44 .command.run -rw-r--r--. 1 1000 root 3236 Jun 8 09:44 .command.sh -rw-r--r--. 1 1000 root 0 Jun 8 09:44 .command.trace -rw-r--r--. 1 1000 root 674965 Jun 8 09:44 aih-tih-sc-242a7d-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 10714998 Jun 8 09:44 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 8 09:44 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 8 09:44 nextflow-bin -rw-r--r--. 1 1000 root 4128 Jun 8 09:44 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-242a7d-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 1812 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 1812 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 169 of 1812 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 111 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: 7 pass (CALL=1), 1805 fail (CALL=0) Total fusions: 1812 (all rows retained) Added FILTER column: PASS=7, FAIL=1805 ✓ Verified: All 216 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 1812 Pass (CALL=1): 7 (0.4%) Fail (CALL=0): 1805 (99.6%) Blacklist Flagging: Total blacklisted: 216 ✓ All 216 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 895 Excluded SpliceType: INCL_NON_REF_SPLICE: 603 Blacklisted: 105 Read count too low: 2 < 8: 67 Blacklisted; aih_curated_blacklist score(3): 64 aih_curated_blacklist score(3): 44 Excluded annotation pattern: HGNC_GENEFAM: 19 aih_curated_blacklist score(5): 2 Excluded annotation pattern: GTEx_recurrent_StarF2019: 2 Read count too low: 7 < 8: 1 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 1 pass, 810 fail (total: 811) ONLY_REF_SPLICE: 6 pass, 995 fail (total: 1001) Read Count Statistics: Fusions with < 3 total reads: 1743 Of these, 1743 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 1812 CALL=1 (pass): 7 CALL=0 (fail): 1805 ✓ Passing fusions (CALL=1) exported to: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================