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/b1/9bfcf0ab593190e5b730a17e0ba0b8/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/b74d395033576acc36426e99e88246/659_SP-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/9bfcf0ab593190e5b730a17e0ba0b8/.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 ==> STAGING COMPLETE (6 inputs) === DEBUGGING INFORMATION === Current working directory: /tmp/nxf.MQJIGjrdPK Input files: - starfusion_tsv: 659_SP-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.MQJIGjrdPK/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.MQJIGjrdPK/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64864 drwx------. 3 1000 root 4096 Jun 4 21:53 . drwxrwxrwx. 4 root root 86 Jun 4 21:53 .. -rw-r--r--. 1 1000 root 0 Jun 4 21:53 .command.err -rw-r--r--. 1 1000 root 880 Jun 4 21:53 .command.out -rw-r--r--. 1 1000 root 14573 Jun 4 21:53 .command.run -rw-r--r--. 1 1000 root 3212 Jun 4 21:53 .command.sh -rw-r--r--. 1 1000 root 0 Jun 4 21:53 .command.trace -rw-r--r--. 1 1000 root 883051 Jun 4 21:53 659_SP-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 10714998 Jun 4 21:53 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 4 21:53 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 4 21:53 nextflow-bin -rw-r--r--. 1 1000 root 4132 Jun 4 21:53 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_SP-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 2902 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 2902 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 296 of 2902 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 168 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: 3 pass (CALL=1), 2899 fail (CALL=0) Total fusions: 2902 (all rows retained) Added FILTER column: PASS=3, FAIL=2899 ✓ Verified: All 359 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 2902 Pass (CALL=1): 3 (0.1%) Fail (CALL=0): 2899 (99.9%) Blacklist Flagging: Total blacklisted: 359 ✓ All 359 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 1756 Excluded SpliceType: INCL_NON_REF_SPLICE: 661 Blacklisted: 191 Blacklisted; aih_curated_blacklist score(3): 104 aih_curated_blacklist score(3): 58 Read count too low: 2 < 8: 46 Excluded annotation pattern: HGNC_GENEFAM: 43 Excluded annotation pattern: GTEx_recurrent_StarF2019: 8 Excluded annotation pattern: DGD_PARALOGS: 7 Does not meet inclusion criteria: 5 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 0 pass, 1131 fail (total: 1131) ONLY_REF_SPLICE: 3 pass, 1768 fail (total: 1771) Read Count Statistics: Fusions with < 3 total reads: 2725 Of these, 2725 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: 659_SP-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 2902 CALL=1 (pass): 3 CALL=0 (fail): 2899 ✓ Passing fusions (CALL=1) exported to: 659_SP-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: 659_SP-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================