.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION_FILTER (tih_rna_sample_00729_B23MVV7LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/43e21b8663349139f76d1fe4317fcf/.command.log
Size: 6.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION_FILTER (tih_rna_sample_00729_B23MVV7LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/5ebb720526efe20f07fc417769bc7f/tih_rna_sample_00729_B23MVV7LT4_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/4f/43e21b8663349139f76d1fe4317fcf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/43e21b8663349139f76d1fe4317fcf/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-7324c8a8-f474-426a-a5c9-715912777f94/9e/b170941eb870c1f39c858900dfb3d4/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.5UtZvliiPF
Input files:
  - starfusion_tsv: tih_rna_sample_00729_B23MVV7LT4_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.5UtZvliiPF/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.5UtZvliiPF/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

=== CURRENT DIRECTORY CONTENTS ===
total 65156
drwx------. 3 1000 root     4096 Jun  8 09:54 .
drwxrwxrwx. 4 root root       86 Jun  8 09:54 ..
-rw-r--r--. 1 1000 root        0 Jun  8 09:54 .command.err
-rw-r--r--. 1 1000 root      884 Jun  8 09:54 .command.out
-rw-r--r--. 1 1000 root    14589 Jun  8 09:54 .command.run
-rw-r--r--. 1 1000 root     3236 Jun  8 09:54 .command.sh
-rw-r--r--. 1 1000 root        0 Jun  8 09:54 .command.trace
-rw-r--r--. 1 1000 root 10714998 Jun  8 09:54 blacklist_breakpoint_database_2026-04-27.tsv
-rw-r--r--. 1 1000 root 54779787 Jun  8 09:54 blacklist_hg38_GRCh38_v2.4.0.tsv.gz
drwxr-xr-x. 3 1000 root     4096 Jun  8 09:54 nextflow-bin
-rw-r--r--. 1 1000 root     4128 Jun  8 09:54 starfusion_filter_config.yaml
-rw-r--r--. 1 1000 root  1179819 Jun  8 09:54 tih_rna_sample_00729_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.tsv

=== 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: tih_rna_sample_00729_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.tsv
  ✓ Loaded: 3611 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: 3610 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 274 of 3611 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 152 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: 7 pass (CALL=1), 3604 fail (CALL=0)
  Total fusions: 3611 (all rows retained)
  Added FILTER column: PASS=7, FAIL=3604

✓ Verified: All 325 blacklisted fusions have CALL=0

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

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

Total fusions: 3611
  Pass (CALL=1): 7 (0.2%)
  Fail (CALL=0): 3604 (99.8%)

Blacklist Flagging:
  Total blacklisted: 325
  ✓ All 325 blacklisted fusions have CALL=0

Failure Reasons (top 10):
  Read count too low: 1 < 8: 2396
  Excluded SpliceType: INCL_NON_REF_SPLICE: 778
  Blacklisted: 173
  Blacklisted; aih_curated_blacklist score(3): 101
  Read count too low: 2 < 8: 51
  aih_curated_blacklist score(3): 47
  Excluded annotation pattern: HGNC_GENEFAM: 33
  Excluded annotation pattern: GTEx_recurrent_StarF2019: 6
  Read count too low: 3 < 8: 4
  Excluded annotation pattern: ConjoinG: 4

Breakdown by SpliceType:
  INCL_NON_REF_SPLICE: 2 pass, 1203 fail (total: 1205)
  NO_JUNCTION_READS_IDENTIFIED: 0 pass, 1 fail (total: 1)
  ONLY_REF_SPLICE: 5 pass, 2400 fail (total: 2405)

Read Count Statistics:
  Fusions with < 3 total reads: 3476
  Of these, 3476 have CALL=0

================================================================================
STEP 6: EXPORTING RESULTS
================================================================================
✓ Results exported to: tih_rna_sample_00729_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv
  Total fusions: 3611
  CALL=1 (pass): 7
  CALL=0 (fail): 3604
✓ Passing fusions (CALL=1) exported to: tih_rna_sample_00729_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
✓ Summary exported to: tih_rna_sample_00729_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt

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