File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/817e982b6beb428589e77b3d82452b/.command.log
Size
5.1 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONREPORT_WORKFLOW:FUSIONREPORT (FFPE_V4_0002_RNA_0001_B23MVV7LT4_1)
Attempt

Content

View in new tab 
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/0c8d30eea0194ffa39dd7528beeac6/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-7324c8a8-f474-426a-a5c9-715912777f94/c4/140ab148cdcf1ed9bdffe91f534e47/dummy_file_fusioncatcher.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/817e982b6beb428589e77b3d82452b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/817e982b6beb428589e77b3d82452b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/fusion_report_db
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/b65a34e3041cf9fc4d8f1d37021325/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
==> STAGING COMPLETE (6 inputs)

Running application...
FGFR3--TACC3
starfusion
arriba
TMPRSS2--ERG
starfusion
arriba
TPM3--NTRK1
starfusion
arriba
LMNA--NTRK1
starfusion
arriba
ETV6--NTRK3
starfusion
arriba
FGFR3--BAIAP2L1
starfusion
arriba
NCOA4--RET
starfusion
arriba
CD74--ROS1
starfusion
CCDC6--RET
starfusion
arriba
KIF5B--RET
starfusion
arriba
SLC45A3--BRAF
starfusion
arriba
SLC34A2--ROS1
starfusion
arriba
PAX8--PPARG
starfusion
arriba
EGFR--SEPTIN14
starfusion
arriba
TFG--NTRK1
starfusion
arriba
EML4--ALK
starfusion
arriba
TLK2P1--AC110079.1
starfusion
TLK2--FAM157A
starfusion
arriba
AC015911.9--SLFN12L
arriba
STX16--NPEPL1
arriba
TVP23C--CDRT4
arriba

  0%|          | 0/21 [00:00<?, ?it/s]
Processing FGFR3--TACC3:   0%|          | 0/21 [00:00<?, ?it/s]
Processing FGFR3--TACC3:   5%|▍         | 1/21 [00:00<00:02,  9.26it/s]
Processing TMPRSS2--ERG:   5%|▍         | 1/21 [00:00<00:02,  9.26it/s]
Processing TMPRSS2--ERG:  10%|▉         | 2/21 [00:00<00:02,  9.49it/s]
Processing TPM3--NTRK1:  10%|▉         | 2/21 [00:00<00:02,  9.49it/s] 
Processing TPM3--NTRK1:  14%|█▍        | 3/21 [00:00<00:01,  9.56it/s]
Processing LMNA--NTRK1:  14%|█▍        | 3/21 [00:00<00:01,  9.56it/s]
Processing LMNA--NTRK1:  19%|█▉        | 4/21 [00:00<00:01,  9.60it/s]
Processing ETV6--NTRK3:  19%|█▉        | 4/21 [00:00<00:01,  9.60it/s]
Processing ETV6--NTRK3:  24%|██▍       | 5/21 [00:00<00:01,  9.62it/s]
Processing FGFR3--BAIAP2L1:  24%|██▍       | 5/21 [00:00<00:01,  9.62it/s]
Processing FGFR3--BAIAP2L1:  29%|██▊       | 6/21 [00:00<00:01,  9.63it/s]
Processing NCOA4--RET:  29%|██▊       | 6/21 [00:00<00:01,  9.63it/s]     
Processing NCOA4--RET:  33%|███▎      | 7/21 [00:00<00:01,  9.64it/s]
Processing CD74--ROS1:  33%|███▎      | 7/21 [00:00<00:01,  9.64it/s]
Processing CD74--ROS1:  38%|███▊      | 8/21 [00:00<00:01,  9.64it/s]
Processing CCDC6--RET:  38%|███▊      | 8/21 [00:00<00:01,  9.64it/s]
Processing CCDC6--RET:  43%|████▎     | 9/21 [00:00<00:01,  9.65it/s]
Processing KIF5B--RET:  43%|████▎     | 9/21 [00:00<00:01,  9.65it/s]
Processing KIF5B--RET:  48%|████▊     | 10/21 [00:01<00:01,  9.65it/s]
Processing SLC45A3--BRAF:  48%|████▊     | 10/21 [00:01<00:01,  9.65it/s]
Processing SLC45A3--BRAF:  52%|█████▏    | 11/21 [00:01<00:01,  9.65it/s]
Processing SLC34A2--ROS1:  52%|█████▏    | 11/21 [00:01<00:01,  9.65it/s]
Processing SLC34A2--ROS1:  57%|█████▋    | 12/21 [00:01<00:00,  9.65it/s]
Processing PAX8--PPARG:  57%|█████▋    | 12/21 [00:01<00:00,  9.65it/s]  
Processing PAX8--PPARG:  62%|██████▏   | 13/21 [00:01<00:00,  9.65it/s]
Processing EGFR--SEPTIN14:  62%|██████▏   | 13/21 [00:01<00:00,  9.65it/s]
Processing EGFR--SEPTIN14:  67%|██████▋   | 14/21 [00:01<00:00,  9.65it/s]
Processing TFG--NTRK1:  67%|██████▋   | 14/21 [00:01<00:00,  9.65it/s]    
Processing TFG--NTRK1:  71%|███████▏  | 15/21 [00:01<00:00,  9.65it/s]
Processing EML4--ALK:  71%|███████▏  | 15/21 [00:01<00:00,  9.65it/s] 
Processing EML4--ALK:  76%|███████▌  | 16/21 [00:01<00:00,  9.65it/s]
Processing TLK2P1--AC110079.1:  76%|███████▌  | 16/21 [00:01<00:00,  9.65it/s]
Processing TLK2P1--AC110079.1:  81%|████████  | 17/21 [00:01<00:00,  9.66it/s]
Processing TLK2--FAM157A:  81%|████████  | 17/21 [00:01<00:00,  9.66it/s]     
Processing TLK2--FAM157A:  86%|████████▌ | 18/21 [00:01<00:00,  9.65it/s]
Processing AC015911.9--SLFN12L:  86%|████████▌ | 18/21 [00:01<00:00,  9.65it/s]
Processing AC015911.9--SLFN12L:  90%|█████████ | 19/21 [00:01<00:00,  9.66it/s]
Processing STX16--NPEPL1:  90%|█████████ | 19/21 [00:01<00:00,  9.66it/s]      
Processing STX16--NPEPL1:  95%|█████████▌| 20/21 [00:02<00:00,  9.65it/s]
Processing TVP23C--CDRT4:  95%|█████████▌| 20/21 [00:02<00:00,  9.65it/s]
Processing TVP23C--CDRT4: 100%|██████████| 21/21 [00:02<00:00,  9.65it/s]
Processing TVP23C--CDRT4: 100%|██████████| 21/21 [00:02<00:00,  9.63it/s]
cat: fusion_report_db/DB-timestamp.txt: No such file or directory