Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/54bed3ee5c632b065f56f09f6c0562/tih_rna_sample_00602_B23MVV7LT4_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/1f/162a80a43259445ff417e598f511a9/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/162a80a43259445ff417e598f511a9/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-7324c8a8-f474-426a-a5c9-715912777f94/9e/b170941eb870c1f39c858900dfb3d4/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.xyEJYITfjR Input files: - starfusion_tsv: tih_rna_sample_00602_B23MVV7LT4_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.xyEJYITfjR/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.xyEJYITfjR/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 65076 drwx------. 3 1000 root 4096 Jun 8 10:18 . drwxrwxrwx. 4 root root 86 Jun 8 10:18 .. -rw-r--r--. 1 1000 root 0 Jun 8 10:18 .command.err -rw-r--r--. 1 1000 root 884 Jun 8 10:18 .command.out -rw-r--r--. 1 1000 root 14589 Jun 8 10:18 .command.run -rw-r--r--. 1 1000 root 3236 Jun 8 10:18 .command.sh -rw-r--r--. 1 1000 root 0 Jun 8 10:18 .command.trace -rw-r--r--. 1 1000 root 10714998 Jun 8 10:18 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 8 10:18 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 8 10:18 nextflow-bin -rw-r--r--. 1 1000 root 4128 Jun 8 10:18 starfusion_filter_config.yaml -rw-r--r--. 1 1000 root 1098526 Jun 8 10:18 tih_rna_sample_00602_B23MVV7LT4_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_00602_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 2964 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 2964 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 244 of 2964 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 129 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: 5 pass (CALL=1), 2959 fail (CALL=0) Total fusions: 2964 (all rows retained) Added FILTER column: PASS=5, FAIL=2959 ✓ Verified: All 292 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 2964 Pass (CALL=1): 5 (0.2%) Fail (CALL=0): 2959 (99.8%) Blacklist Flagging: Total blacklisted: 292 ✓ All 292 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 1925 Excluded SpliceType: INCL_NON_REF_SPLICE: 622 Blacklisted: 163 Blacklisted; aih_curated_blacklist score(3): 81 Read count too low: 2 < 8: 56 aih_curated_blacklist score(3): 43 Excluded annotation pattern: HGNC_GENEFAM: 38 Excluded annotation pattern: GTEx_recurrent_StarF2019: 7 Read count too low: 3 < 8: 5 Read count too low: 6 < 8: 4 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 2 pass, 1087 fail (total: 1089) ONLY_REF_SPLICE: 3 pass, 1872 fail (total: 1875) Read Count Statistics: Fusions with < 3 total reads: 2809 Of these, 2809 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: tih_rna_sample_00602_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 2964 CALL=1 (pass): 5 CALL=0 (fail): 2959 ✓ Passing fusions (CALL=1) exported to: tih_rna_sample_00602_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: tih_rna_sample_00602_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================