File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/d49c98729421cb821bb903b77a16e9/.command.log
Size
2.6 KB
Task
NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION_FILTER (aih-tih-sc-6473fb-R1_B23WHYVLT4_1)
Attempt

Content

View in new tab 
  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/b4/d49c98729421cb821bb903b77a16e9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/d49c98729421cb821bb903b77a16e9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/3cf837baa16d8b0041cacf267decb9/aih-tih-sc-6473fb-R1_B23WHYVLT4_1.starfusion.starfusion.fusion_predictions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-8900cb43-4dca-49ac-a290-1d176a2e0012/4f/77edb82c6b530e8b635dd5e8cb776f/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.e16YY5yyRc
Input files:
  - starfusion_tsv: aih-tih-sc-6473fb-R1_B23WHYVLT4_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.e16YY5yyRc/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.e16YY5yyRc/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

=== CURRENT DIRECTORY CONTENTS ===
total 64668
drwx------. 3 1000 root     4096 Jun  8 09:41 .
drwxrwxrwx. 4 root root       86 Jun  8 09:41 ..
-rw-r--r--. 1 1000 root        0 Jun  8 09:41 .command.err
-rw-r--r--. 1 1000 root      884 Jun  8 09:41 .command.out
-rw-r--r--. 1 1000 root    14589 Jun  8 09:41 .command.run
-rw-r--r--. 1 1000 root     3236 Jun  8 09:41 .command.sh
-rw-r--r--. 1 1000 root        0 Jun  8 09:41 .command.trace
-rw-r--r--. 1 1000 root   682232 Jun  8 09:41 aih-tih-sc-6473fb-R1_B23WHYVLT4_1.starfusion.starfusion.fusion_predictions.tsv
-rw-r--r--. 1 1000 root 10714998 Jun  8 09:41 blacklist_breakpoint_database_2026-04-27.tsv
-rw-r--r--. 1 1000 root 54779787 Jun  8 09:41 blacklist_hg38_GRCh38_v2.4.0.tsv.gz
drwxr-xr-x. 3 1000 root     4096 Jun  8 09:41 nextflow-bin
-rw-r--r--. 1 1000 root     4128 Jun  8 09:41 starfusion_filter_config.yaml

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

=== Running filter script ===