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/b9/5894251ff8a60905ab1987a34c2c56/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/5894251ff8a60905ab1987a34c2c56/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/ab35c84678c5688213e4f95a3d9365/659_cIX-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-0c31b8cc-cacb-407a-8f2b-eb2d8317e249/c7/8e5f4192e27cefa89cd0b9856a9a6d/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.rBGMpx2Z37 Input files: - starfusion_tsv: 659_cIX-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.rBGMpx2Z37/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.rBGMpx2Z37/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64956 drwx------. 3 1000 root 4096 Jun 8 09:45 . drwxrwxrwx. 4 root root 86 Jun 8 09:45 .. -rw-r--r--. 1 1000 root 0 Jun 8 09:45 .command.err -rw-r--r--. 1 1000 root 881 Jun 8 09:45 .command.out -rw-r--r--. 1 1000 root 14577 Jun 8 09:45 .command.run -rw-r--r--. 1 1000 root 3218 Jun 8 09:45 .command.sh -rw-r--r--. 1 1000 root 0 Jun 8 09:45 .command.trace -rw-r--r--. 1 1000 root 978721 Jun 8 09:45 659_cIX-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 10714998 Jun 8 09:45 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 8 09:45 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 8 09:45 nextflow-bin -rw-r--r--. 1 1000 root 4128 Jun 8 09:45 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_cIX-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 3157 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 3157 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 3157 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 162 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: 18 pass (CALL=1), 3139 fail (CALL=0) Total fusions: 3157 (all rows retained) Added FILTER column: PASS=18, FAIL=3139 ✓ Verified: All 337 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 3157 Pass (CALL=1): 18 (0.6%) Fail (CALL=0): 3139 (99.4%) Blacklist Flagging: Total blacklisted: 337 ✓ All 337 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 2007 Excluded SpliceType: INCL_NON_REF_SPLICE: 646 Blacklisted: 175 Blacklisted; aih_curated_blacklist score(3): 111 Excluded annotation pattern: HGNC_GENEFAM: 52 aih_curated_blacklist score(3): 47 Read count too low: 2 < 8: 47 Read count too low: 3 < 8: 17 Read count too low: 5 < 8: 7 Excluded annotation pattern: GTEx_recurrent_StarF2019: 6 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 4 pass, 1150 fail (total: 1154) ONLY_REF_SPLICE: 14 pass, 1989 fail (total: 2003) Read Count Statistics: Fusions with < 3 total reads: 2947 Of these, 2947 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: 659_cIX-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 3157 CALL=1 (pass): 18 CALL=0 (fail): 3139 ✓ Passing fusions (CALL=1) exported to: 659_cIX-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: 659_cIX-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================