Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-eb5d3959-7137-45a9-9f26-41f9201dcf7f/9d/27ef28c083f97facc14cc8364be994/dummy_file_fusioncatcher.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/17217f4331e02f75f1dfc5b5ea88b4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/17217f4331e02f75f1dfc5b5ea88b4/.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/bd/095bb6a57dea9fbc7ed0ace9bc6135/FFPE_V4_0002_RNA_0002_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/c9627e88842a128d2707b135bd7dbb/FFPE_V4_0002_RNA_0002_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.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
SLC45A3--BRAF
starfusion
arriba
CCDC6--RET
starfusion
arriba
KIF5B--RET
starfusion
arriba
CD74--ROS1
starfusion
SLC34A2--ROS1
starfusion
arriba
PAX8--PPARG
starfusion
arriba
EGFR--SEPTIN14
starfusion
arriba
TFG--NTRK1
starfusion
arriba
EML4--ALK
starfusion
arriba
STX16--NPEPL1
starfusion
arriba
TLK2P1--AC110079.1
starfusion
ACTBP6--ACTB
starfusion
TLK2--AC240565.1
starfusion
CDV3--MT-RNR2
starfusion
TVP23C--CDRT4
arriba
SOGA3--KIAA0408
arriba

  0%|          | 0/23 [00:00<?, ?it/s]
Processing FGFR3--TACC3:   0%|          | 0/23 [00:00<?, ?it/s]
Processing FGFR3--TACC3:   4%|▍         | 1/23 [00:00<00:02,  9.24it/s]
Processing TMPRSS2--ERG:   4%|▍         | 1/23 [00:00<00:02,  9.24it/s]
Processing TMPRSS2--ERG:   9%|▊         | 2/23 [00:00<00:02,  9.48it/s]
Processing TPM3--NTRK1:   9%|▊         | 2/23 [00:00<00:02,  9.48it/s] 
Processing TPM3--NTRK1:  13%|█▎        | 3/23 [00:00<00:02,  9.56it/s]
Processing LMNA--NTRK1:  13%|█▎        | 3/23 [00:00<00:02,  9.56it/s]
Processing LMNA--NTRK1:  17%|█▋        | 4/23 [00:00<00:01,  9.59it/s]
Processing ETV6--NTRK3:  17%|█▋        | 4/23 [00:00<00:01,  9.59it/s]
Processing ETV6--NTRK3:  22%|██▏       | 5/23 [00:00<00:01,  9.62it/s]
Processing FGFR3--BAIAP2L1:  22%|██▏       | 5/23 [00:00<00:01,  9.62it/s]
Processing FGFR3--BAIAP2L1:  26%|██▌       | 6/23 [00:00<00:01,  9.63it/s]
Processing NCOA4--RET:  26%|██▌       | 6/23 [00:00<00:01,  9.63it/s]     
Processing NCOA4--RET:  30%|███       | 7/23 [00:00<00:01,  9.64it/s]
Processing SLC45A3--BRAF:  30%|███       | 7/23 [00:00<00:01,  9.64it/s]
Processing SLC45A3--BRAF:  35%|███▍      | 8/23 [00:00<00:01,  9.64it/s]
Processing CCDC6--RET:  35%|███▍      | 8/23 [00:00<00:01,  9.64it/s]   
Processing CCDC6--RET:  39%|███▉      | 9/23 [00:00<00:01,  9.64it/s]
Processing KIF5B--RET:  39%|███▉      | 9/23 [00:00<00:01,  9.64it/s]
Processing KIF5B--RET:  43%|████▎     | 10/23 [00:01<00:01,  9.65it/s]
Processing CD74--ROS1:  43%|████▎     | 10/23 [00:01<00:01,  9.65it/s]
Processing CD74--ROS1:  48%|████▊     | 11/23 [00:01<00:01,  9.65it/s]
Processing SLC34A2--ROS1:  48%|████▊     | 11/23 [00:01<00:01,  9.65it/s]
Processing SLC34A2--ROS1:  52%|█████▏    | 12/23 [00:01<00:01,  9.65it/s]
Processing PAX8--PPARG:  52%|█████▏    | 12/23 [00:01<00:01,  9.65it/s]  
Processing PAX8--PPARG:  57%|█████▋    | 13/23 [00:01<00:01,  9.65it/s]
Processing EGFR--SEPTIN14:  57%|█████▋    | 13/23 [00:01<00:01,  9.65it/s]
Processing EGFR--SEPTIN14:  61%|██████    | 14/23 [00:01<00:00,  9.65it/s]
Processing TFG--NTRK1:  61%|██████    | 14/23 [00:01<00:00,  9.65it/s]    
Processing TFG--NTRK1:  65%|██████▌   | 15/23 [00:01<00:00,  9.65it/s]
Processing EML4--ALK:  65%|██████▌   | 15/23 [00:01<00:00,  9.65it/s] 
Processing EML4--ALK:  70%|██████▉   | 16/23 [00:01<00:00,  9.64it/s]
Processing STX16--NPEPL1:  70%|██████▉   | 16/23 [00:01<00:00,  9.64it/s]
Processing STX16--NPEPL1:  74%|███████▍  | 17/23 [00:01<00:00,  9.65it/s]
Processing TLK2P1--AC110079.1:  74%|███████▍  | 17/23 [00:01<00:00,  9.65it/s]
Processing TLK2P1--AC110079.1:  78%|███████▊  | 18/23 [00:01<00:00,  9.65it/s]
Processing ACTBP6--ACTB:  78%|███████▊  | 18/23 [00:01<00:00,  9.65it/s]      
Processing ACTBP6--ACTB:  83%|████████▎ | 19/23 [00:01<00:00,  9.65it/s]
Processing TLK2--AC240565.1:  83%|████████▎ | 19/23 [00:01<00:00,  9.65it/s]
Processing TLK2--AC240565.1:  87%|████████▋ | 20/23 [00:02<00:00,  9.65it/s]
Processing CDV3--MT-RNR2:  87%|████████▋ | 20/23 [00:02<00:00,  9.65it/s]   
Processing CDV3--MT-RNR2:  91%|█████████▏| 21/23 [00:02<00:00,  9.65it/s]
Processing TVP23C--CDRT4:  91%|█████████▏| 21/23 [00:02<00:00,  9.65it/s]
Processing TVP23C--CDRT4:  96%|█████████▌| 22/23 [00:02<00:00,  9.65it/s]
Processing SOGA3--KIAA0408:  96%|█████████▌| 22/23 [00:02<00:00,  9.65it/s]
Processing SOGA3--KIAA0408: 100%|██████████| 23/23 [00:02<00:00,  9.65it/s]
Processing SOGA3--KIAA0408: 100%|██████████| 23/23 [00:02<00:00,  9.63it/s]
cat: fusion_report_db/DB-timestamp.txt: No such file or directory