Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/a9e5d29243daab26ae846848926081/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.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/da/ee53864971ca9f6164ef4c7bc35460/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/ee53864971ca9f6164ef4c7bc35460/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-6ef41cd9-2e18-4687-842c-3f6f49c5643f/48/32e6a611973bf3895a673373080bf1/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.KDbenYXaAE
Input files:
  - starfusion_tsv: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.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.KDbenYXaAE/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.KDbenYXaAE/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

=== CURRENT DIRECTORY CONTENTS ===
total 65108
drwx------. 3 1000 root     4096 May 28 22:49 .
drwxrwxrwx. 4 root root       86 May 28 22:49 ..
-rw-r--r--. 1 1000 root        0 May 28 22:49 .command.err
-rw-r--r--. 1 1000 root      888 May 28 22:49 .command.out
-rw-r--r--. 1 1000 root    14605 May 28 22:49 .command.run
-rw-r--r--. 1 1000 root     3260 May 28 22:49 .command.sh
-rw-r--r--. 1 1000 root        0 May 28 22:49 .command.trace
-rw-r--r--. 1 1000 root  1132259 May 28 22:49 SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.starfusion.starfusion.fusion_predictions.tsv
-rw-r--r--. 1 1000 root 10714998 May 28 22:49 blacklist_breakpoint_database_2026-04-27.tsv
-rw-r--r--. 1 1000 root 54779787 May 28 22:49 blacklist_hg38_GRCh38_v2.4.0.tsv.gz
drwxr-xr-x. 4 1000 root     4096 May 28 22:49 nextflow-bin
-rw-r--r--. 1 1000 root     4132 May 28 22:49 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: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.starfusion.starfusion.fusion_predictions.tsv
  ✓ Loaded: 1031 fusions

================================================================================
STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT
================================================================================
✓ Converted to breakpoint_ID format: 1031 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 139 of 1031 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 78 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: 45 pass (CALL=1), 986 fail (CALL=0)
  Total fusions: 1031 (all rows retained)
  Added FILTER column: PASS=45, FAIL=986

✓ Verified: All 165 blacklisted fusions have CALL=0

================================================================================
STEP 5: GENERATING SUMMARY STATISTICS
================================================================================

================================================================================
FILTERING SUMMARY
================================================================================

Total fusions: 1031
  Pass (CALL=1): 45 (4.4%)
  Fail (CALL=0): 986 (95.6%)

Blacklist Flagging:
  Total blacklisted: 165
  ✓ All 165 blacklisted fusions have CALL=0

Failure Reasons (top 10):
  Read count too low: 1 < 8: 506
  Excluded SpliceType: INCL_NON_REF_SPLICE: 256
  Blacklisted: 87
  Blacklisted; aih_curated_blacklist score(3): 52
  aih_curated_blacklist score(3): 25
  Read count too low: 2 < 8: 14
  Read count too low: 3 < 8: 9
  Excluded annotation pattern: HGNC_GENEFAM: 7
  Read count too low: 5 < 8: 6
  Does not meet inclusion criteria: 5

Breakdown by SpliceType:
  INCL_NON_REF_SPLICE: 1 pass, 467 fail (total: 468)
  ONLY_REF_SPLICE: 44 pass, 519 fail (total: 563)

Read Count Statistics:
  Fusions with < 3 total reads: 863
  Of these, 863 have CALL=0

================================================================================
STEP 6: EXPORTING RESULTS
================================================================================
✓ Results exported to: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv
  Total fusions: 1031
  CALL=1 (pass): 45
  CALL=0 (fail): 986
✓ Passing fusions (CALL=1) exported to: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
✓ Summary exported to: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt

================================================================================
✓ FILTERING COMPLETE
================================================================================