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/9b/4864bc0dbd04a292f1ed2141b10f48/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/4864bc0dbd04a292f1ed2141b10f48/.command.run 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 Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/6ee7e4c587166a41364c5eeaf2105f/659_On-T1-TRNA-2_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv ==> STAGING COMPLETE (6 inputs) === DEBUGGING INFORMATION === Current working directory: /tmp/nxf.tcXfhNlcis Input files: - starfusion_tsv: 659_On-T1-TRNA-2_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.tcXfhNlcis/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.tcXfhNlcis/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64728 drwx------. 3 1000 root 4096 Jun 8 10:06 . drwxrwxrwx. 4 root root 86 Jun 8 10:06 .. -rw-r--r--. 1 1000 root 0 Jun 8 10:06 .command.err -rw-r--r--. 1 1000 root 880 Jun 8 10:06 .command.out -rw-r--r--. 1 1000 root 14573 Jun 8 10:06 .command.run -rw-r--r--. 1 1000 root 3212 Jun 8 10:06 .command.sh -rw-r--r--. 1 1000 root 0 Jun 8 10:06 .command.trace -rw-r--r--. 1 1000 root 744057 Jun 8 10:06 659_On-T1-TRNA-2_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 10714998 Jun 8 10:06 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 8 10:06 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 8 10:06 nextflow-bin -rw-r--r--. 1 1000 root 4128 Jun 8 10:06 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_On-T1-TRNA-2_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 2290 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 2290 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 269 of 2290 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 135 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), 2274 fail (CALL=0) Total fusions: 2290 (all rows retained) Added FILTER column: PASS=16, FAIL=2274 ✓ Verified: All 320 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 2290 Pass (CALL=1): 16 (0.7%) Fail (CALL=0): 2274 (99.3%) Blacklist Flagging: Total blacklisted: 320 ✓ All 320 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 1304 Excluded SpliceType: INCL_NON_REF_SPLICE: 541 Blacklisted: 185 Blacklisted; aih_curated_blacklist score(3): 84 aih_curated_blacklist score(3): 46 Read count too low: 2 < 8: 40 Excluded annotation pattern: HGNC_GENEFAM: 30 Read count too low: 3 < 8: 15 Excluded annotation pattern: GTEx_recurrent_StarF2019: 7 Excluded annotation pattern: DGD_PARALOGS: 6 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 3 pass, 977 fail (total: 980) ONLY_REF_SPLICE: 13 pass, 1297 fail (total: 1310) Read Count Statistics: Fusions with < 3 total reads: 2110 Of these, 2110 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: 659_On-T1-TRNA-2_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 2290 CALL=1 (pass): 16 CALL=0 (fail): 2274 ✓ Passing fusions (CALL=1) exported to: 659_On-T1-TRNA-2_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: 659_On-T1-TRNA-2_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================