Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/c422b40c51da2010ee16d542ab0e49/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.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/1e/e50109878a9d2e209702aecfb54d7d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/e50109878a9d2e209702aecfb54d7d/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-fe242a7f-c5b9-4d3f-88fa-f3e739280d3a/f8/f9224e55c50c449a43c8a740b583b3/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.8Qe3moJgom Input files: - starfusion_tsv: 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.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.8Qe3moJgom/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.8Qe3moJgom/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64352 drwx------. 3 1000 root 4096 Jun 8 08:52 . drwxrwxrwx. 4 root root 86 Jun 8 08:52 .. -rw-r--r--. 1 1000 root 0 Jun 8 08:52 .command.err -rw-r--r--. 1 1000 root 886 Jun 8 08:52 .command.out -rw-r--r--. 1 1000 root 14597 Jun 8 08:52 .command.run -rw-r--r--. 1 1000 root 3248 Jun 8 08:52 .command.sh -rw-r--r--. 1 1000 root 0 Jun 8 08:52 .command.trace -rw-r--r--. 1 1000 root 360154 Jun 8 08:52 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 10714998 Jun 8 08:52 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 8 08:52 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 8 08:52 nextflow-bin -rw-r--r--. 1 1000 root 4128 Jun 8 08:52 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: 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 1325 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 1325 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 116 of 1325 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 80 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: 4 pass (CALL=1), 1321 fail (CALL=0) Total fusions: 1325 (all rows retained) Added FILTER column: PASS=4, FAIL=1321 ✓ Verified: All 158 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 1325 Pass (CALL=1): 4 (0.3%) Fail (CALL=0): 1321 (99.7%) Blacklist Flagging: Total blacklisted: 158 ✓ All 158 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 646 Excluded SpliceType: INCL_NON_REF_SPLICE: 468 Blacklisted: 78 aih_curated_blacklist score(3): 39 Blacklisted; aih_curated_blacklist score(3): 38 Excluded annotation pattern: HGNC_GENEFAM: 21 Read count too low: 2 < 8: 15 Excluded annotation pattern: DGD_PARALOGS: 4 Excluded annotation pattern: GTEx_recurrent_StarF2019: 2 Read count too low: 5 < 8: 2 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 1 pass, 811 fail (total: 812) ONLY_REF_SPLICE: 3 pass, 510 fail (total: 513) Read Count Statistics: Fusions with < 3 total reads: 1271 Of these, 1271 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 1325 CALL=1 (pass): 4 CALL=0 (fail): 1321 ✓ Passing fusions (CALL=1) exported to: 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================