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/99/53b8e12c62da8e3472b27647f1c267/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/53b8e12c62da8e3472b27647f1c267/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-bba2394f-ea06-4038-829e-f0bb41c45b0f/3c/3b7a2778bcfaa6267940faa13afda3/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/8c/986880e0abad0f48c48f9d0eabc2f3/659_buD-T1-TRNA-1_A23MVY2LT4_2.starfusion.starfusion.fusion_predictions.tsv
==> STAGING COMPLETE (6 inputs)
=== DEBUGGING INFORMATION ===
Current working directory: /tmp/nxf.S6cz0njGbg
Input files:
- starfusion_tsv: 659_buD-T1-TRNA-1_A23MVY2LT4_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.S6cz0njGbg/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.S6cz0njGbg/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
=== CURRENT DIRECTORY CONTENTS ===
total 64956
drwx------. 3 1000 root 4096 Jun 8 09:50 .
drwxrwxrwx. 4 root root 86 Jun 8 09:50 ..
-rw-r--r--. 1 1000 root 0 Jun 8 09:50 .command.err
-rw-r--r--. 1 1000 root 881 Jun 8 09:50 .command.out
-rw-r--r--. 1 1000 root 14577 Jun 8 09:50 .command.run
-rw-r--r--. 1 1000 root 3218 Jun 8 09:50 .command.sh
-rw-r--r--. 1 1000 root 0 Jun 8 09:50 .command.trace
-rw-r--r--. 1 1000 root 974856 Jun 8 09:50 659_buD-T1-TRNA-1_A23MVY2LT4_2.starfusion.starfusion.fusion_predictions.tsv
-rw-r--r--. 1 1000 root 10714998 Jun 8 09:50 blacklist_breakpoint_database_2026-04-27.tsv
-rw-r--r--. 1 1000 root 54779787 Jun 8 09:50 blacklist_hg38_GRCh38_v2.4.0.tsv.gz
drwxr-xr-x. 3 1000 root 4096 Jun 8 09:50 nextflow-bin
-rw-r--r--. 1 1000 root 4128 Jun 8 09:50 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: 659_buD-T1-TRNA-1_A23MVY2LT4_2.starfusion.starfusion.fusion_predictions.tsv
✓ Loaded: 3515 fusions
================================================================================
STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT
================================================================================
✓ Converted to breakpoint_ID format: 3515 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 281 of 3515 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 164 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: 24 pass (CALL=1), 3491 fail (CALL=0)
Total fusions: 3515 (all rows retained)
Added FILTER column: PASS=24, FAIL=3491
✓ Verified: All 339 blacklisted fusions have CALL=0
================================================================================
STEP 5: GENERATING SUMMARY STATISTICS
================================================================================
================================================================================
FILTERING SUMMARY
================================================================================
Total fusions: 3515
Pass (CALL=1): 24 (0.7%)
Fail (CALL=0): 3491 (99.3%)
Blacklist Flagging:
Total blacklisted: 339
✓ All 339 blacklisted fusions have CALL=0
Failure Reasons (top 10):
Read count too low: 1 < 8: 2279
Excluded SpliceType: INCL_NON_REF_SPLICE: 730
Blacklisted: 175
Blacklisted; aih_curated_blacklist score(3): 106
aih_curated_blacklist score(3): 53
Read count too low: 2 < 8: 49
Excluded annotation pattern: HGNC_GENEFAM: 49
Read count too low: 3 < 8: 11
Excluded annotation pattern: DGD_PARALOGS: 10
Excluded annotation pattern: GTEx_recurrent_StarF2019: 10
Breakdown by SpliceType:
INCL_NON_REF_SPLICE: 8 pass, 1249 fail (total: 1257)
ONLY_REF_SPLICE: 16 pass, 2242 fail (total: 2258)
Read Count Statistics:
Fusions with < 3 total reads: 3359
Of these, 3359 have CALL=0
================================================================================
STEP 6: EXPORTING RESULTS
================================================================================
✓ Results exported to: 659_buD-T1-TRNA-1_A23MVY2LT4_2.starfusion.starfusion.fusion_predictions.filtered.tsv
Total fusions: 3515
CALL=1 (pass): 24
CALL=0 (fail): 3491
✓ Passing fusions (CALL=1) exported to: 659_buD-T1-TRNA-1_A23MVY2LT4_2.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
✓ Summary exported to: 659_buD-T1-TRNA-1_A23MVY2LT4_2.starfusion.starfusion.fusion_predictions.filter_summary.txt
================================================================================
✓ FILTERING COMPLETE
================================================================================