Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/c895a7eebb723bebf8becd4caf290b/rna_s1200_S21.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/fa/d511588b40872fadee6462f87bc360/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/d511588b40872fadee6462f87bc360/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-4f0d47f6-dcb1-4599-b3b8-38811c184130/28/8a6032d67cb12bf8d2a05257e28f4b/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.Xoo38OkEO3 Input files: - starfusion_tsv: rna_s1200_S21.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.Xoo38OkEO3/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.Xoo38OkEO3/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin === CURRENT DIRECTORY CONTENTS === total 64144 drwx------. 3 1000 root 4096 Jun 6 00:13 . drwxrwxrwx. 4 root root 86 Jun 6 00:13 .. -rw-r--r--. 1 1000 root 0 Jun 6 00:13 .command.err -rw-r--r--. 1 1000 root 864 Jun 6 00:13 .command.out -rw-r--r--. 1 1000 root 14509 Jun 6 00:13 .command.run -rw-r--r--. 1 1000 root 3116 Jun 6 00:13 .command.sh -rw-r--r--. 1 1000 root 0 Jun 6 00:13 .command.trace -rw-r--r--. 1 1000 root 10714998 Jun 6 00:13 blacklist_breakpoint_database_2026-04-27.tsv -rw-r--r--. 1 1000 root 54779787 Jun 6 00:13 blacklist_hg38_GRCh38_v2.4.0.tsv.gz drwxr-xr-x. 3 1000 root 4096 Jun 6 00:13 nextflow-bin -rw-r--r--. 1 1000 root 145983 Jun 6 00:13 rna_s1200_S21.starfusion.starfusion.fusion_predictions.tsv -rw-r--r--. 1 1000 root 4128 Jun 6 00:13 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: rna_s1200_S21.starfusion.starfusion.fusion_predictions.tsv ✓ Loaded: 493 fusions ================================================================================ STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT ================================================================================ ⚠ Warning: 1 rows have invalid breakpoint_ID (will be skipped in blacklist flagging) ✓ Converted to breakpoint_ID format: 492 valid, 1 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 34 of 493 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 20 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: 7 pass (CALL=1), 486 fail (CALL=0) Total fusions: 493 (all rows retained) Added FILTER column: PASS=7, FAIL=486 ✓ Verified: All 42 blacklisted fusions have CALL=0 ================================================================================ STEP 5: GENERATING SUMMARY STATISTICS ================================================================================ ================================================================================ FILTERING SUMMARY ================================================================================ Total fusions: 493 Pass (CALL=1): 7 (1.4%) Fail (CALL=0): 486 (98.6%) Blacklist Flagging: Total blacklisted: 42 ✓ All 42 blacklisted fusions have CALL=0 Failure Reasons (top 10): Read count too low: 1 < 8: 315 Excluded SpliceType: INCL_NON_REF_SPLICE: 112 Blacklisted: 22 Blacklisted; aih_curated_blacklist score(3): 12 aih_curated_blacklist score(3): 8 Excluded annotation pattern: HGNC_GENEFAM: 7 Read count too low: 2 < 8: 3 Read count too low: 7 < 8: 2 Excluded annotation pattern: GTEx_recurrent_StarF2019: 2 Read count too low: 6 < 8: 1 Breakdown by SpliceType: INCL_NON_REF_SPLICE: 0 pass, 167 fail (total: 167) NO_JUNCTION_READS_IDENTIFIED: 0 pass, 1 fail (total: 1) ONLY_REF_SPLICE: 7 pass, 318 fail (total: 325) Read Count Statistics: Fusions with < 3 total reads: 478 Of these, 478 have CALL=0 ================================================================================ STEP 6: EXPORTING RESULTS ================================================================================ ✓ Results exported to: rna_s1200_S21.starfusion.starfusion.fusion_predictions.filtered.tsv Total fusions: 493 CALL=1 (pass): 7 CALL=0 (fail): 486 ✓ Passing fusions (CALL=1) exported to: rna_s1200_S21.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv ✓ Summary exported to: rna_s1200_S21.starfusion.starfusion.fusion_predictions.filter_summary.txt ================================================================================ ✓ FILTERING COMPLETE ================================================================================