Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/8678ddd531a0963c2a78d413a22cde/ColoN_FFPE_L01_RNA_01_B23LG7FLT4_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/d3/faafe4d81e14859f4ed998e338b24d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/faafe4d81e14859f4ed998e338b24d/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/58/2f66683c63e8e0a2b7a3c46113f09d/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.JJdzIoKdSN Input files: - starfusion_tsv: ColoN_FFPE_L01_RNA_01_B23LG7FLT4_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.JJdzIoKdSN/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.JJdzIoKdSN/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64272 drwx------. 3 1000 root 4096 Jun 8 10:59 . drwxrwxrwx. 4 root root 86 Jun 8 10:59 .. -rw-r--r--. 1 1000 root 0 Jun 8 10:59 .command.err -rw-r--r--. 1 1000 root 885 Jun 8 10:59 .command.out -rw-r--r--. 1 1000 root 14593 Jun 8 10:59 .command.run -rw-r--r--. 1 1000 root 3242 Jun 8 10:59 .command.sh -rw-r--r--. 1 1000 root 0 Jun 8 10:59 .command.trace -rw-r--r--. 1 1000 root 275900 Jun 8 10:59 ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 10714998 Jun 8 10:59 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 8 10:59 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 8 10:59 nextflow-bin -rw-r--r--. 1 1000 root 4128 Jun 8 10:59 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: ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 845 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ✓ Converted to breakpoint_ID format: 845 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 76 of 845 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 63 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: 0 pass (CALL=1), 845 fail (CALL=0) Total fusions: 845 (all rows retained) Added FILTER column: PASS=0, FAIL=845 ✓ Verified: All 112 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 845 Pass (CALL=1): 0 (0.0%) Fail (CALL=0): 845 (100.0%) Blacklist Flagging: Total blacklisted: 112 ✓ All 112 blacklisted fusions have CALL=0 Failure Reasons (top 10): Excluded SpliceType: INCL_NON_REF_SPLICE: 479 Read count too low: 1 < 8: 204 Blacklisted: 49 aih_curated_blacklist score(3): 36 Blacklisted; aih_curated_blacklist score(3): 27 Read count too low: 2 < 8: 24 Excluded annotation pattern: HGNC_GENEFAM: 19 Read count too low: 3 < 8: 4 Excluded annotation pattern: DGD_PARALOGS: 3 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 0 pass, 610 fail (total: 610) ONLY_REF_SPLICE: 0 pass, 235 fail (total: 235) Read Count Statistics: Fusions with < 3 total reads: 808 Of these, 808 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 845 CALL=1 (pass): 0 CALL=0 (fail): 845 ✓ Empty pass_only file created (no passing fusions): ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================