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/ff/a068d2f4e966c6ee265c0156e83a78/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/a068d2f4e966c6ee265c0156e83a78/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-13dfb8f7-c999-4ef0-9260-22ba79cf647d/b9/18377b9883182c957fab33d641aa83/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/03/11f448df50d1d4cffd7d705078d61c/BVT_FFPE_TRNA_crv_01_A23WKFTLT4_3.starfusion.starfusion.fusion_predictions.tsv
==> STAGING COMPLETE (6 inputs)
=== DEBUGGING INFORMATION ===
Current working directory: /tmp/nxf.TyXY0RGcT5
Input files:
- starfusion_tsv: BVT_FFPE_TRNA_crv_01_A23WKFTLT4_3.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.TyXY0RGcT5/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.TyXY0RGcT5/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
=== CURRENT DIRECTORY CONTENTS ===
total 66616
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 2676655 Jun 8 10:18 BVT_FFPE_TRNA_crv_01_A23WKFTLT4_3.starfusion.starfusion.fusion_predictions.tsv
-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
=== 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: BVT_FFPE_TRNA_crv_01_A23WKFTLT4_3.starfusion.starfusion.fusion_predictions.tsv
✓ Loaded: 3405 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: 3404 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 319 of 3405 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 174 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: 10 pass (CALL=1), 3395 fail (CALL=0)
Total fusions: 3405 (all rows retained)
Added FILTER column: PASS=10, FAIL=3395
✓ Verified: All 381 blacklisted fusions have CALL=0
================================================================================
STEP 5: GENERATING SUMMARY STATISTICS
================================================================================
================================================================================
FILTERING SUMMARY
================================================================================
Total fusions: 3405
Pass (CALL=1): 10 (0.3%)
Fail (CALL=0): 3395 (99.7%)
Blacklist Flagging:
Total blacklisted: 381
✓ All 381 blacklisted fusions have CALL=0
Failure Reasons (top 10):
Read count too low: 1 < 8: 2092
Excluded SpliceType: INCL_NON_REF_SPLICE: 790
Blacklisted: 207
Blacklisted; aih_curated_blacklist score(3): 112
aih_curated_blacklist score(3): 59
Read count too low: 2 < 8: 52
Excluded annotation pattern: HGNC_GENEFAM: 37
Read count too low: 3 < 8: 12
Excluded annotation pattern: GTEx_recurrent_StarF2019: 11
Excluded annotation pattern: DGD_PARALOGS: 9
Breakdown by SpliceType:
INCL_NON_REF_SPLICE: 1 pass, 1339 fail (total: 1340)
NO_JUNCTION_READS_IDENTIFIED: 0 pass, 1 fail (total: 1)
ONLY_REF_SPLICE: 9 pass, 2055 fail (total: 2064)
Read Count Statistics:
Fusions with < 3 total reads: 3257
Of these, 3257 have CALL=0
================================================================================
STEP 6: EXPORTING RESULTS
================================================================================
✓ Results exported to: BVT_FFPE_TRNA_crv_01_A23WKFTLT4_3.starfusion.starfusion.fusion_predictions.filtered.tsv
Total fusions: 3405
CALL=1 (pass): 10
CALL=0 (fail): 3395
✓ Passing fusions (CALL=1) exported to: BVT_FFPE_TRNA_crv_01_A23WKFTLT4_3.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
✓ Summary exported to: BVT_FFPE_TRNA_crv_01_A23WKFTLT4_3.starfusion.starfusion.fusion_predictions.filter_summary.txt
================================================================================
✓ FILTERING COMPLETE
================================================================================