Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/0b9ceb918e7943cdbbe6e97fa24911/tih_rna_sample_00163_B23WHTKLT4_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/a6/6aa0d90e772d622d342a080a6fc917/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/6aa0d90e772d622d342a080a6fc917/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ed/cac574e455bdcf55a155d65fb3ed05/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.vQn992W7Qi Input files: - starfusion_tsv: tih_rna_sample_00163_B23WHTKLT4_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.vQn992W7Qi/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.vQn992W7Qi/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64924 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 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 -rw-r--r--. 1 1000 root 944129 Jun 8 08:49 tih_rna_sample_00163_B23WHTKLT4_1.starfusion.starfusion.fusion_predictions.tsv === 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: tih_rna_sample_00163_B23WHTKLT4_1.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 2965 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 2965 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 272 of 2965 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: 7 pass (CALL=1), 2958 fail (CALL=0) Total fusions: 2965 (all rows retained) Added FILTER column: PASS=7, FAIL=2958 ✓ Verified: All 318 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 2965 Pass (CALL=1): 7 (0.2%) Fail (CALL=0): 2958 (99.8%) Blacklist Flagging: Total blacklisted: 318 ✓ All 318 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 1789 Excluded SpliceType: INCL_NON_REF_SPLICE: 732 Blacklisted: 170 Blacklisted; aih_curated_blacklist score(3): 102 Read count too low: 2 < 8: 61 aih_curated_blacklist score(3): 43 Excluded annotation pattern: HGNC_GENEFAM: 31 Read count too low: 3 < 8: 9 Read count too low: 4 < 8: 6 Excluded annotation pattern: DGD_PARALOGS: 5 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 1 pass, 1096 fail (total: 1097) ONLY_REF_SPLICE: 6 pass, 1862 fail (total: 1868) Read Count Statistics: Fusions with < 3 total reads: 2844 Of these, 2844 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: tih_rna_sample_00163_B23WHTKLT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 2965 CALL=1 (pass): 7 CALL=0 (fail): 2958 ✓ Passing fusions (CALL=1) exported to: tih_rna_sample_00163_B23WHTKLT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: tih_rna_sample_00163_B23WHTKLT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================