.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION_FILTER (RT4_FFPE_RNA_0001_B23LG7FLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/06fef581e26a2fa85974c18dfd903d/.command.log
Size: 6.6 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION_FILTER (RT4_FFPE_RNA_0001_B23LG7FLT4_2)
Attempt
Content

  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/80/06fef581e26a2fa85974c18dfd903d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/06fef581e26a2fa85974c18dfd903d/.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
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/c643a286056a1a5fd2b11620bf1c2d/RT4_FFPE_RNA_0001_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.tsv
==> STAGING COMPLETE (6 inputs)

=== DEBUGGING INFORMATION ===
Current working directory: /tmp/nxf.SJfhNKuasm
Input files:
  - starfusion_tsv: RT4_FFPE_RNA_0001_B23LG7FLT4_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.SJfhNKuasm/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.SJfhNKuasm/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

=== CURRENT DIRECTORY CONTENTS ===
total 65328
drwx------. 3 1000 root     4096 May 28 22:33 .
drwxrwxrwx. 4 root root       70 May 28 22:33 ..
-rw-r--r--. 1 1000 root        0 May 28 22:33 .command.err
-rw-r--r--. 1 1000 root      881 May 28 22:33 .command.out
-rw-r--r--. 1 1000 root    14577 May 28 22:33 .command.run
-rw-r--r--. 1 1000 root     3218 May 28 22:33 .command.sh
-rw-r--r--. 1 1000 root        0 May 28 22:33 .command.trace
-rw-r--r--. 1 1000 root  1356060 May 28 22:33 RT4_FFPE_RNA_0001_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.tsv
-rw-r--r--. 1 1000 root 10714998 May 28 22:33 blacklist_breakpoint_database_2026-04-27.tsv
-rw-r--r--. 1 1000 root 54779787 May 28 22:33 blacklist_hg38_GRCh38_v2.4.0.tsv.gz
drwxr-xr-x. 4 1000 root     4096 May 28 22:33 nextflow-bin
-rw-r--r--. 1 1000 root     4132 May 28 22:33 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: RT4_FFPE_RNA_0001_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.tsv
  ✓ Loaded: 2288 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: 2287 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 182 of 2288 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 111 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: 15 pass (CALL=1), 2273 fail (CALL=0)
  Total fusions: 2288 (all rows retained)
  Added FILTER column: PASS=15, FAIL=2273

✓ Verified: All 223 blacklisted fusions have CALL=0

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

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

Total fusions: 2288
  Pass (CALL=1): 15 (0.7%)
  Fail (CALL=0): 2273 (99.3%)

Blacklist Flagging:
  Total blacklisted: 223
  ✓ All 223 blacklisted fusions have CALL=0

Failure Reasons (top 10):
  Read count too low: 1 < 8: 1445
  Excluded SpliceType: INCL_NON_REF_SPLICE: 508
  Blacklisted: 112
  Blacklisted; aih_curated_blacklist score(3): 70
  aih_curated_blacklist score(3): 38
  Excluded annotation pattern: HGNC_GENEFAM: 33
  Read count too low: 2 < 8: 28
  Read count too low: 3 < 8: 12
  Read count too low: 4 < 8: 5
  Excluded annotation pattern: DGD_PARALOGS: 5

Breakdown by SpliceType:
  INCL_NON_REF_SPLICE: 4 pass, 852 fail (total: 856)
  NO_JUNCTION_READS_IDENTIFIED: 0 pass, 1 fail (total: 1)
  ONLY_REF_SPLICE: 11 pass, 1420 fail (total: 1431)

Read Count Statistics:
  Fusions with < 3 total reads: 2136
  Of these, 2136 have CALL=0

================================================================================
STEP 6: EXPORTING RESULTS
================================================================================
✓ Results exported to: RT4_FFPE_RNA_0001_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.filtered.tsv
  Total fusions: 2288
  CALL=1 (pass): 15
  CALL=0 (fail): 2273
✓ Passing fusions (CALL=1) exported to: RT4_FFPE_RNA_0001_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
✓ Summary exported to: RT4_FFPE_RNA_0001_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.filter_summary.txt

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