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/08/c8ad13aaaebc6b3b7c3ceda5912442/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/9d1a542b3a3789b9d02137791bac07/dna_s765.starfusion.starfusion.fusion_predictions.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/c8ad13aaaebc6b3b7c3ceda5912442/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-fff52061-f714-4c14-bb2c-bf5549840817/fa/1b0e8aa2b9bc076955000ae8fedff3/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.fgNlhyXoDN
Input files:
- starfusion_tsv: dna_s765.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.fgNlhyXoDN/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.fgNlhyXoDN/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
=== CURRENT DIRECTORY CONTENTS ===
total 64064
drwx------. 3 1000 root 4096 Jun 8 07:47 .
drwxrwxrwx. 4 root root 70 Jun 8 07:47 ..
-rw-r--r--. 1 1000 root 0 Jun 8 07:47 .command.err
-rw-r--r--. 1 1000 root 859 Jun 8 07:47 .command.out
-rw-r--r--. 1 1000 root 14489 Jun 8 07:47 .command.run
-rw-r--r--. 1 1000 root 3086 Jun 8 07:47 .command.sh
-rw-r--r--. 1 1000 root 0 Jun 8 07:47 .command.trace
-rw-r--r--. 1 1000 root 10714998 Jun 8 07:47 blacklist_breakpoint_database_2026-04-27.tsv
-rw-r--r--. 1 1000 root 54779787 Jun 8 07:47 blacklist_hg38_GRCh38_v2.4.0.tsv.gz
-rw-r--r--. 1 1000 root 62206 Jun 8 07:47 dna_s765.starfusion.starfusion.fusion_predictions.tsv
drwxr-xr-x. 3 1000 root 4096 Jun 8 07:47 nextflow-bin
-rw-r--r--. 1 1000 root 4128 Jun 8 07:47 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: dna_s765.starfusion.starfusion.fusion_predictions.tsv
✓ Loaded: 212 fusions
================================================================================
STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT
================================================================================
⚠ Warning: 2 rows have invalid breakpoint_ID (will be skipped in blacklist flagging)
✓ Converted to breakpoint_ID format: 210 valid, 2 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 8 of 212 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 6 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), 212 fail (CALL=0)
Total fusions: 212 (all rows retained)
Added FILTER column: PASS=0, FAIL=212
✓ Verified: All 12 blacklisted fusions have CALL=0
================================================================================
STEP 5: GENERATING SUMMARY STATISTICS
================================================================================
================================================================================
FILTERING SUMMARY
================================================================================
Total fusions: 212
Pass (CALL=1): 0 (0.0%)
Fail (CALL=0): 212 (100.0%)
Blacklist Flagging:
Total blacklisted: 12
✓ All 12 blacklisted fusions have CALL=0
Failure Reasons (top 10):
Excluded SpliceType: INCL_NON_REF_SPLICE: 106
Read count too low: 1 < 8: 85
Blacklisted: 6
Read count too low: 2 < 8: 5
aih_curated_blacklist score(3): 4
Blacklisted; aih_curated_blacklist score(3): 2
Read count too low: 7 < 8: 1
Read count too low: 6 < 8: 1
Read count too low: 4 < 8: 1
Excluded annotation pattern: HGNC_GENEFAM: 1
Breakdown by SpliceType:
INCL_NON_REF_SPLICE: 0 pass, 210 fail (total: 210)
NO_JUNCTION_READS_IDENTIFIED: 0 pass, 2 fail (total: 2)
Read Count Statistics:
Fusions with < 3 total reads: 188
Of these, 188 have CALL=0
================================================================================
STEP 6: EXPORTING RESULTS
================================================================================
✓ Results exported to: dna_s765.starfusion.starfusion.fusion_predictions.filtered.tsv
Total fusions: 212
CALL=1 (pass): 0
CALL=0 (fail): 212
✓ Empty pass_only file created (no passing fusions): dna_s765.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
✓ Summary exported to: dna_s765.starfusion.starfusion.fusion_predictions.filter_summary.txt
================================================================================
✓ FILTERING COMPLETE
================================================================================