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/72/0c8d30eea0194ffa39dd7528beeac6/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/0c8d30eea0194ffa39dd7528beeac6/.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 Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/1dd31cfafad339719de4285fb12666/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.tsv ==> STAGING COMPLETE (6 inputs) === DEBUGGING INFORMATION === Current working directory: /tmp/nxf.ibg1dgqbP5 Input files: - starfusion_tsv: FFPE_V4_0002_RNA_0001_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.ibg1dgqbP5/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.ibg1dgqbP5/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 65364 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 885 Jun 8 09:45 .command.out -rw-r--r--. 1 1000 root 14593 Jun 8 09:45 .command.run -rw-r--r--. 1 1000 root 3242 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 1394950 Jun 8 09:45 FFPE_V4_0002_RNA_0001_B23MVV7LT4_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: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 3355 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 3355 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 192 of 3355 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 119 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), 3337 fail (CALL=0) Total fusions: 3355 (all rows retained) Added FILTER column: PASS=18, FAIL=3337 ✓ Verified: All 248 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 3355 Pass (CALL=1): 18 (0.5%) Fail (CALL=0): 3337 (99.5%) Blacklist Flagging: Total blacklisted: 248 ✓ All 248 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 2383 Excluded SpliceType: INCL_NON_REF_SPLICE: 612 Blacklisted: 129 Blacklisted; aih_curated_blacklist score(3): 62 aih_curated_blacklist score(3): 52 Read count too low: 2 < 8: 51 Excluded annotation pattern: HGNC_GENEFAM: 24 Read count too low: 3 < 8: 7 Excluded annotation pattern: GTEx_recurrent_StarF2019: 4 Excluded annotation pattern: Greger_Normal: 3 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 1 pass, 992 fail (total: 993) ONLY_REF_SPLICE: 17 pass, 2345 fail (total: 2362) Read Count Statistics: Fusions with < 3 total reads: 3241 Of these, 3241 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 3355 CALL=1 (pass): 18 CALL=0 (fail): 3337 ✓ Passing fusions (CALL=1) exported to: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================