.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION_FILTER (659_dkd-T1-TRNA-1_B23MHV2LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/7d2482551e104a0800341b068d315c/.command.log
Size: 6.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION_FILTER (659_dkd-T1-TRNA-1_B23MHV2LT4_1)
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/5b/7d2482551e104a0800341b068d315c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/7d2482551e104a0800341b068d315c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/87836d56b6995ad204f34ff0127b0d/659_dkd-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-40cc52c0-5bec-40b6-b04d-c64c51f55eff/32/72884c9bc45220d4a6a63dced576ff/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.NWD3yIgPjR
Input files:
  - starfusion_tsv: 659_dkd-T1-TRNA-1_B23MHV2LT4_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.NWD3yIgPjR/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.NWD3yIgPjR/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

=== CURRENT DIRECTORY CONTENTS ===
total 64004
drwx------. 3 1000 root     4096 Jun  4 20:23 .
drwxrwxrwx. 4 root root       86 Jun  4 20:23 ..
-rw-r--r--. 1 1000 root        0 Jun  4 20:23 .command.err
-rw-r--r--. 1 1000 root      881 Jun  4 20:23 .command.out
-rw-r--r--. 1 1000 root    14577 Jun  4 20:23 .command.run
-rw-r--r--. 1 1000 root     3218 Jun  4 20:23 .command.sh
-rw-r--r--. 1 1000 root        0 Jun  4 20:23 .command.trace
-rw-r--r--. 1 1000 root      246 Jun  4 20:23 659_dkd-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv
-rw-r--r--. 1 1000 root 10714998 Jun  4 20:23 blacklist_breakpoint_database_2026-04-27.tsv
-rw-r--r--. 1 1000 root 54779787 Jun  4 20:23 blacklist_hg38_GRCh38_v2.4.0.tsv.gz
drwxr-xr-x. 3 1000 root     4096 Jun  4 20:23 nextflow-bin
-rw-r--r--. 1 1000 root     4132 Jun  4 20:23 starfusion_filter_config.yaml

=== PROJECT DIRECTORY INFO ===
NXF_PROJECT_DIR: not set
baseDir: not set

=== Running filter script ===
/tmp/nxf.NWD3yIgPjR/nextflow-bin/filter_starfusion_main.py:161: RuntimeWarning: invalid value encountered in scalar divide
  print(f"  Pass (CALL=1): {summary['call_pass']} ({100*summary['call_pass']/summary['total_fusions']:.1f}%)")
/tmp/nxf.NWD3yIgPjR/nextflow-bin/filter_starfusion_main.py:162: RuntimeWarning: invalid value encountered in scalar divide
  print(f"  Fail (CALL=0): {summary['call_fail']} ({100*summary['call_fail']/summary['total_fusions']:.1f}%)")
/tmp/nxf.NWD3yIgPjR/nextflow-bin/filter_starfusion_main.py:214: RuntimeWarning: invalid value encountered in scalar divide
  f.write(f"Pass (CALL=1): {summary['call_pass']} ({100*summary['call_pass']/summary['total_fusions']:.1f}%)\n")
/tmp/nxf.NWD3yIgPjR/nextflow-bin/filter_starfusion_main.py:215: RuntimeWarning: invalid value encountered in scalar divide
  f.write(f"Fail (CALL=0): {summary['call_fail']} ({100*summary['call_fail']/summary['total_fusions']:.1f}%)\n")

================================================================================
STEP 1: LOADING STAR-FUSION PREDICTIONS
================================================================================
Loading STAR-Fusion predictions from: 659_dkd-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.tsv
  ✓ Loaded: 0 fusions

================================================================================
STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT
================================================================================
✓ Converted to breakpoint_ID format: 0 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 0.0 of 0 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 0 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), 0 fail (CALL=0)
  Total fusions: 0 (all rows retained)
  Added FILTER column: PASS=0, FAIL=0

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

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

Total fusions: 0
  Pass (CALL=1): 0 (nan%)
  Fail (CALL=0): 0 (nan%)

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

================================================================================
STEP 6: EXPORTING RESULTS
================================================================================
✓ Results exported to: 659_dkd-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv
  Total fusions: 0
  CALL=1 (pass): 0
  CALL=0 (fail): 0
✓ Empty pass_only file created (no passing fusions): 659_dkd-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
✓ Summary exported to: 659_dkd-T1-TRNA-1_B23MHV2LT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt

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