Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/1bd95a0f3bf10e8ed20150b276a23e/.command.sh 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/d2/1bd95a0f3bf10e8ed20150b276a23e/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-40cc52c0-5bec-40b6-b04d-c64c51f55eff/32/72884c9bc45220d4a6a63dced576ff/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/53/f9c2b244dac9410056168dffebe3d8/659_dRe-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv ==> STAGING COMPLETE (6 inputs) === DEBUGGING INFORMATION === Current working directory: /tmp/nxf.xHwAHrjYVe Input files: - starfusion_tsv: 659_dRe-T1-TRNA-1_B23MHV2LT4_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.xHwAHrjYVe/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.xHwAHrjYVe/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64976 drwx------. 3 1000 root 4096 Jun 4 21:55 . drwxrwxrwx. 4 root root 86 Jun 4 21:55 .. -rw-r--r--. 1 1000 root 0 Jun 4 21:55 .command.err -rw-r--r--. 1 1000 root 881 Jun 4 21:55 .command.out -rw-r--r--. 1 1000 root 14577 Jun 4 21:55 .command.run -rw-r--r--. 1 1000 root 3218 Jun 4 21:55 .command.sh -rw-r--r--. 1 1000 root 0 Jun 4 21:55 .command.trace -rw-r--r--. 1 1000 root 995426 Jun 4 21:55 659_dRe-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 10714998 Jun 4 21:55 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 4 21:55 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 4 21:55 nextflow-bin -rw-r--r--. 1 1000 root 4132 Jun 4 21:55 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: 659_dRe-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 3353 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 3353 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 286 of 3353 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 148 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: 16 pass (CALL=1), 3337 fail (CALL=0) Total fusions: 3353 (all rows retained) Added FILTER column: PASS=16, FAIL=3337 ✓ Verified: All 332 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 3353 Pass (CALL=1): 16 (0.5%) Fail (CALL=0): 3337 (99.5%) Blacklist Flagging: Total blacklisted: 332 ✓ All 332 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 2200 Excluded SpliceType: INCL_NON_REF_SPLICE: 661 Blacklisted: 184 Blacklisted; aih_curated_blacklist score(3): 101 Read count too low: 2 < 8: 55 Excluded annotation pattern: HGNC_GENEFAM: 44 aih_curated_blacklist score(3): 43 Read count too low: 3 < 8: 12 Excluded annotation pattern: DGD_PARALOGS: 8 Read count too low: 4 < 8: 7 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 0 pass, 1146 fail (total: 1146) ONLY_REF_SPLICE: 16 pass, 2191 fail (total: 2207) Read Count Statistics: Fusions with < 3 total reads: 3180 Of these, 3180 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: 659_dRe-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 3353 CALL=1 (pass): 16 CALL=0 (fail): 3337 ✓ Passing fusions (CALL=1) exported to: 659_dRe-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: 659_dRe-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================