File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4d5b4104000d4feca9b6bd7eebba5d/.command.log
Size
10.6 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONREPORT_WORKFLOW:FUSIONREPORT (A673_FFPE_RNA_0001_B23LG7FLT4_2)
Attempt

Content

View in new tab 
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/db/27263bb39e3cbdc9558e9c4c8a77db/dummy_file_fusioncatcher.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4d5b4104000d4feca9b6bd7eebba5d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4d5b4104000d4feca9b6bd7eebba5d/.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/10/edd10b4cfbc2cc9ca4a5a2fa84704b/A673_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/f344daa0960a633c8991ca264aeec8/A673_FFPE_RNA_0001_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
==> STAGING COMPLETE (6 inputs)

Running application...
EWSR1--FLI1
starfusion
arriba
SMURF2P1--SP2
starfusion
arriba
SUPT20H--CHRDL2
starfusion
arriba
CYP7B1--LINC01414
starfusion
arriba
NPM1--MT-RNR2
starfusion
TLK2--AC240565.1
starfusion
TLK2P1--AC110079.1
starfusion
SELENOOLP--HOOK1
starfusion
LINC00221--SPG7
starfusion
PCDHGA6--PCDHGC5
arriba
PCDHGA6--PCDHGA8
arriba
PCDHGA6--PCDHGC4
arriba
PCDHGA6--PCDHGB6
arriba
PCDHGA6--PCDHGA10
arriba
PCDHGA6--PCDHGA12
arriba
PCDHGA6--PCDHGC3
arriba
PCDHGA6--PCDHGB7
arriba
PCDHGA6--PCDHGA11
arriba
PCDHGA6--PCDHGA9
arriba
PCDHA11--PCDHA13
arriba
PCDHA11--PCDHAC1
arriba
PCDHA11--PCDHAC2
arriba
PCDHA6--PCDHAC2
arriba
PCDHA6--PCDHA13
arriba
PCDHA6--PCDHAC1
arriba
SPG7--PLSCR5
arriba
SPG7--AC092957.1
arriba
PCDHGB2--PCDHGC5
arriba
PCDHGB2--PCDHGA8
arriba
PCDHGB2--PCDHGC4
arriba
PCDHGB2--PCDHGB6
arriba
PCDHGB2--PCDHGA10
arriba
PCDHGB2--PCDHGA12
arriba
PCDHGB2--PCDHGC3
arriba
PCDHGB2--PCDHGB7
arriba
PCDHGB2--PCDHGA11
arriba
PCDHGB2--PCDHGA9
arriba
PCDHA8--PCDHA10
arriba
PCDHA10--PCDHAC2
arriba
PCDHA10--PCDHAC1
arriba
PCDHA10--PCDHA13
arriba
RBM14--RBM4
arriba
SUCLA2--AL158828.1
arriba
SUCLA2--AL353613.1
arriba
CCDC169--SOHLH2
arriba
SOGA3--KIAA0408
arriba
TMEM132B--TDG
arriba
IGH@-ext--SPG7
arriba
IGH-@-ext--SPG7
arriba

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Processing EWSR1--FLI1:   0%|          | 0/49 [00:00<?, ?it/s]
Processing EWSR1--FLI1:   2%|▏         | 1/49 [00:00<00:05,  9.17it/s]
Processing SMURF2P1--SP2:   2%|▏         | 1/49 [00:00<00:05,  9.17it/s]
Processing SMURF2P1--SP2:   4%|▍         | 2/49 [00:00<00:04,  9.42it/s]
Processing SUPT20H--CHRDL2:   4%|▍         | 2/49 [00:00<00:04,  9.42it/s]
Processing SUPT20H--CHRDL2:   6%|▌         | 3/49 [00:00<00:04,  9.51it/s]
Processing CYP7B1--LINC01414:   6%|▌         | 3/49 [00:00<00:04,  9.51it/s]
Processing CYP7B1--LINC01414:   8%|▊         | 4/49 [00:00<00:04,  9.55it/s]
Processing NPM1--MT-RNR2:   8%|▊         | 4/49 [00:00<00:04,  9.55it/s]    
Processing NPM1--MT-RNR2:  10%|█         | 5/49 [00:00<00:04,  9.56it/s]
Processing TLK2--AC240565.1:  10%|█         | 5/49 [00:00<00:04,  9.56it/s]
Processing TLK2--AC240565.1:  12%|█▏        | 6/49 [00:00<00:04,  9.58it/s]
Processing TLK2P1--AC110079.1:  12%|█▏        | 6/49 [00:00<00:04,  9.58it/s]
Processing TLK2P1--AC110079.1:  14%|█▍        | 7/49 [00:00<00:04,  9.59it/s]
Processing SELENOOLP--HOOK1:  14%|█▍        | 7/49 [00:00<00:04,  9.59it/s]  
Processing SELENOOLP--HOOK1:  16%|█▋        | 8/49 [00:00<00:04,  9.60it/s]
Processing LINC00221--SPG7:  16%|█▋        | 8/49 [00:00<00:04,  9.60it/s] 
Processing LINC00221--SPG7:  18%|█▊        | 9/49 [00:00<00:04,  9.61it/s]
Processing PCDHGA6--PCDHGC5:  18%|█▊        | 9/49 [00:00<00:04,  9.61it/s]
Processing PCDHGA6--PCDHGC5:  20%|██        | 10/49 [00:01<00:04,  9.61it/s]
Processing PCDHGA6--PCDHGA8:  20%|██        | 10/49 [00:01<00:04,  9.61it/s]
Processing PCDHGA6--PCDHGA8:  22%|██▏       | 11/49 [00:01<00:03,  9.61it/s]
Processing PCDHGA6--PCDHGC4:  22%|██▏       | 11/49 [00:01<00:03,  9.61it/s]
Processing PCDHGA6--PCDHGC4:  24%|██▍       | 12/49 [00:01<00:03,  9.61it/s]
Processing PCDHGA6--PCDHGB6:  24%|██▍       | 12/49 [00:01<00:03,  9.61it/s]
Processing PCDHGA6--PCDHGB6:  27%|██▋       | 13/49 [00:01<00:03,  9.61it/s]
Processing PCDHGA6--PCDHGA10:  27%|██▋       | 13/49 [00:01<00:03,  9.61it/s]
Processing PCDHGA6--PCDHGA10:  29%|██▊       | 14/49 [00:01<00:03,  9.62it/s]
Processing PCDHGA6--PCDHGA12:  29%|██▊       | 14/49 [00:01<00:03,  9.62it/s]
Processing PCDHGA6--PCDHGA12:  31%|███       | 15/49 [00:01<00:03,  9.62it/s]
Processing PCDHGA6--PCDHGC3:  31%|███       | 15/49 [00:01<00:03,  9.62it/s] 
Processing PCDHGA6--PCDHGC3:  33%|███▎      | 16/49 [00:01<00:03,  9.62it/s]
Processing PCDHGA6--PCDHGB7:  33%|███▎      | 16/49 [00:01<00:03,  9.62it/s]
Processing PCDHGA6--PCDHGB7:  35%|███▍      | 17/49 [00:01<00:03,  9.62it/s]
Processing PCDHGA6--PCDHGA11:  35%|███▍      | 17/49 [00:01<00:03,  9.62it/s]
Processing PCDHGA6--PCDHGA11:  37%|███▋      | 18/49 [00:01<00:03,  9.62it/s]
Processing PCDHGA6--PCDHGA9:  37%|███▋      | 18/49 [00:01<00:03,  9.62it/s] 
Processing PCDHGA6--PCDHGA9:  39%|███▉      | 19/49 [00:01<00:03,  9.61it/s]
Processing PCDHA11--PCDHA13:  39%|███▉      | 19/49 [00:01<00:03,  9.61it/s]
Processing PCDHA11--PCDHA13:  41%|████      | 20/49 [00:02<00:03,  9.62it/s]
Processing PCDHA11--PCDHAC1:  41%|████      | 20/49 [00:02<00:03,  9.62it/s]
Processing PCDHA11--PCDHAC1:  43%|████▎     | 21/49 [00:02<00:02,  9.62it/s]
Processing PCDHA11--PCDHAC2:  43%|████▎     | 21/49 [00:02<00:02,  9.62it/s]
Processing PCDHA11--PCDHAC2:  45%|████▍     | 22/49 [00:02<00:02,  9.61it/s]
Processing PCDHA6--PCDHAC2:  45%|████▍     | 22/49 [00:02<00:02,  9.61it/s] 
Processing PCDHA6--PCDHAC2:  47%|████▋     | 23/49 [00:02<00:02,  9.61it/s]
Processing PCDHA6--PCDHA13:  47%|████▋     | 23/49 [00:02<00:02,  9.61it/s]
Processing PCDHA6--PCDHA13:  49%|████▉     | 24/49 [00:02<00:02,  9.62it/s]
Processing PCDHA6--PCDHAC1:  49%|████▉     | 24/49 [00:02<00:02,  9.62it/s]
Processing PCDHA6--PCDHAC1:  51%|█████     | 25/49 [00:02<00:02,  9.62it/s]
Processing SPG7--PLSCR5:  51%|█████     | 25/49 [00:02<00:02,  9.62it/s]   
Processing SPG7--PLSCR5:  53%|█████▎    | 26/49 [00:02<00:02,  9.62it/s]
Processing SPG7--AC092957.1:  53%|█████▎    | 26/49 [00:02<00:02,  9.62it/s]
Processing SPG7--AC092957.1:  55%|█████▌    | 27/49 [00:02<00:02,  9.62it/s]
Processing PCDHGB2--PCDHGC5:  55%|█████▌    | 27/49 [00:02<00:02,  9.62it/s]
Processing PCDHGB2--PCDHGC5:  57%|█████▋    | 28/49 [00:02<00:02,  9.62it/s]
Processing PCDHGB2--PCDHGA8:  57%|█████▋    | 28/49 [00:02<00:02,  9.62it/s]
Processing PCDHGB2--PCDHGA8:  59%|█████▉    | 29/49 [00:03<00:02,  9.62it/s]
Processing PCDHGB2--PCDHGC4:  59%|█████▉    | 29/49 [00:03<00:02,  9.62it/s]
Processing PCDHGB2--PCDHGC4:  61%|██████    | 30/49 [00:03<00:01,  9.62it/s]
Processing PCDHGB2--PCDHGB6:  61%|██████    | 30/49 [00:03<00:01,  9.62it/s]
Processing PCDHGB2--PCDHGB6:  63%|██████▎   | 31/49 [00:03<00:01,  9.62it/s]
Processing PCDHGB2--PCDHGA10:  63%|██████▎   | 31/49 [00:03<00:01,  9.62it/s]
Processing PCDHGB2--PCDHGA10:  65%|██████▌   | 32/49 [00:03<00:01,  9.62it/s]
Processing PCDHGB2--PCDHGA12:  65%|██████▌   | 32/49 [00:03<00:01,  9.62it/s]
Processing PCDHGB2--PCDHGA12:  67%|██████▋   | 33/49 [00:03<00:01,  9.62it/s]
Processing PCDHGB2--PCDHGC3:  67%|██████▋   | 33/49 [00:03<00:01,  9.62it/s] 
Processing PCDHGB2--PCDHGC3:  69%|██████▉   | 34/49 [00:03<00:01,  9.61it/s]
Processing PCDHGB2--PCDHGB7:  69%|██████▉   | 34/49 [00:03<00:01,  9.61it/s]
Processing PCDHGB2--PCDHGB7:  71%|███████▏  | 35/49 [00:03<00:01,  9.61it/s]
Processing PCDHGB2--PCDHGA11:  71%|███████▏  | 35/49 [00:03<00:01,  9.61it/s]
Processing PCDHGB2--PCDHGA11:  73%|███████▎  | 36/49 [00:03<00:01,  9.61it/s]
Processing PCDHGB2--PCDHGA9:  73%|███████▎  | 36/49 [00:03<00:01,  9.61it/s] 
Processing PCDHGB2--PCDHGA9:  76%|███████▌  | 37/49 [00:03<00:01,  9.61it/s]
Processing PCDHA8--PCDHA10:  76%|███████▌  | 37/49 [00:03<00:01,  9.61it/s] 
Processing PCDHA8--PCDHA10:  78%|███████▊  | 38/49 [00:03<00:01,  9.61it/s]
Processing PCDHA10--PCDHAC2:  78%|███████▊  | 38/49 [00:03<00:01,  9.61it/s]
Processing PCDHA10--PCDHAC2:  80%|███████▉  | 39/49 [00:04<00:01,  9.61it/s]
Processing PCDHA10--PCDHAC1:  80%|███████▉  | 39/49 [00:04<00:01,  9.61it/s]
Processing PCDHA10--PCDHAC1:  82%|████████▏ | 40/49 [00:04<00:00,  9.61it/s]
Processing PCDHA10--PCDHA13:  82%|████████▏ | 40/49 [00:04<00:00,  9.61it/s]
Processing PCDHA10--PCDHA13:  84%|████████▎ | 41/49 [00:04<00:00,  9.61it/s]
Processing RBM14--RBM4:  84%|████████▎ | 41/49 [00:04<00:00,  9.61it/s]     
Processing RBM14--RBM4:  86%|████████▌ | 42/49 [00:04<00:00,  9.61it/s]
Processing SUCLA2--AL158828.1:  86%|████████▌ | 42/49 [00:04<00:00,  9.61it/s]
Processing SUCLA2--AL158828.1:  88%|████████▊ | 43/49 [00:04<00:00,  9.61it/s]
Processing SUCLA2--AL353613.1:  88%|████████▊ | 43/49 [00:04<00:00,  9.61it/s]
Processing SUCLA2--AL353613.1:  90%|████████▉ | 44/49 [00:04<00:00,  9.61it/s]
Processing CCDC169--SOHLH2:  90%|████████▉ | 44/49 [00:04<00:00,  9.61it/s]   
Processing CCDC169--SOHLH2:  92%|█████████▏| 45/49 [00:04<00:00,  9.61it/s]
Processing SOGA3--KIAA0408:  92%|█████████▏| 45/49 [00:04<00:00,  9.61it/s]
Processing SOGA3--KIAA0408:  94%|█████████▍| 46/49 [00:04<00:00,  9.61it/s]
Processing TMEM132B--TDG:  94%|█████████▍| 46/49 [00:04<00:00,  9.61it/s]  
Processing TMEM132B--TDG:  96%|█████████▌| 47/49 [00:04<00:00,  9.61it/s]
Processing IGH@-ext--SPG7:  96%|█████████▌| 47/49 [00:04<00:00,  9.61it/s]
Processing IGH@-ext--SPG7:  98%|█████████▊| 48/49 [00:04<00:00,  9.61it/s]
Processing IGH-@-ext--SPG7:  98%|█████████▊| 48/49 [00:05<00:00,  9.61it/s]
Processing IGH-@-ext--SPG7: 100%|██████████| 49/49 [00:05<00:00,  9.61it/s]
Processing IGH-@-ext--SPG7: 100%|██████████| 49/49 [00:05<00:00,  9.60it/s]
cat: fusion_report_db/DB-timestamp.txt: No such file or directory