Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/55b1f6d8b3d0384c27ffaedf46a821/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
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/a7/665f60cd3f15a5fce1f211988783ea/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/665f60cd3f15a5fce1f211988783ea/.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/05/adff501251d58efa0725f5bc2c0d09/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
==> STAGING COMPLETE (6 inputs)
[32mRunning application...[0m
SLC34A2--ROS1
starfusion
arriba
MYO5C--SHC4
starfusion
arriba
CCDC6--RET
starfusion
arriba
ANTXR1--AC011897.1
starfusion
arriba
PANK2--MAVS
starfusion
arriba
WAC--SFMBT2
starfusion
arriba
TCF7L2--AL158212.1
starfusion
arriba
PPL--SEC14L5
starfusion
arriba
C18orf25--GREB1L
starfusion
arriba
CENPM--PACSIN2
starfusion
arriba
B9D1--CD82
starfusion
arriba
PEX3--AIG1
starfusion
arriba
ZNF227--GAB2
starfusion
arriba
THAP12--ACO1
starfusion
arriba
EFNA5--IKBKB
starfusion
arriba
FANCA--CDK10
starfusion
arriba
CHMP1A--FANCA
starfusion
DDX1--AC068286.1
starfusion
MGA--GABRB3
starfusion
arriba
TLK2--AC240565.1
starfusion
BCL2L13--EP300
starfusion
arriba
MIPOL1--TTC6
starfusion
arriba
MRPS14--TNR
starfusion
arriba
TLK2P1--AC110079.1
starfusion
ATG16L2--C11orf80
starfusion
arriba
ZDHHC9--AL034405.1
starfusion
arriba
KDM4B--CYP4F22
starfusion
arriba
ANTXR2--TNFSF10
starfusion
WWP2--STARD9
starfusion
CASP8--STRADB
starfusion
SPAG9--MBTD1
starfusion
GOLGA6L10--GOLGA2P6
starfusion
CUL4B--TMEM255A
starfusion
ELF2--EGFLAM
starfusion
arriba
FN1--AC012462.2
starfusion
ANTXR1--Metazoa_SRP
arriba
ANTXR1--RN7SKP168
arriba
ANTXR1--ZFYVE9P2
arriba
TVP23C--CDRT4
arriba
CCNJL--FABP6
arriba
SYNCRIP--SNX14
arriba
PCDHGB2--PCDHGA8
arriba
PCDHGB2--PCDHGC5
arriba
PCDHGB2--PCDHGA11
arriba
PCDHGB2--PCDHGC4
arriba
PCDHGB2--PCDHGA10
arriba
PCDHGB2--PCDHGB6
arriba
PCDHGB2--PCDHGC3
arriba
PCDHGB2--PCDHGA9
arriba
PCDHGB2--PCDHGB7
arriba
PCDHGB2--PCDHGA12
arriba
HERC2--AC018362.1
arriba
HERC2--SNAP23
arriba
RBM14--RBM4
arriba
CMIP--AP001970.1
arriba
CMIP--U8
arriba
HNRNPM--TIMM29
arriba
PCDHA4--PCDHAC2
arriba
PCDHA4--PCDHAC1
arriba
PCDHA4--PCDHA13
arriba
IKBKB--CHRNA6
arriba
IKBKB--THAP1
arriba
SOGA3--KIAA0408
arriba
TRIP10--KDM4B
arriba
CCDC169--SOHLH2
arriba
PPIP5K1--OTUD7A
arriba
KLRC4--KLRK1
arriba
ZNF419--ZNF772
arriba
TLK2--FAM157A
arriba
ROR1--RASSF9
arriba
ROR1--NTS
arriba
RNF216--UNC93B2
arriba
CRYZL2P--SEC16B
arriba
0%| | 0/73 [00:00<?, ?it/s]
Processing SLC34A2--ROS1: 0%| | 0/73 [00:00<?, ?it/s]
Processing SLC34A2--ROS1: 1%|▏ | 1/73 [00:00<00:07, 9.26it/s]
Processing MYO5C--SHC4: 1%|▏ | 1/73 [00:00<00:07, 9.26it/s]
Processing MYO5C--SHC4: 3%|▎ | 2/73 [00:00<00:07, 9.49it/s]
Processing CCDC6--RET: 3%|▎ | 2/73 [00:00<00:07, 9.49it/s]
Processing CCDC6--RET: 4%|▍ | 3/73 [00:00<00:07, 9.56it/s]
Processing ANTXR1--AC011897.1: 4%|▍ | 3/73 [00:00<00:07, 9.56it/s]
Processing ANTXR1--AC011897.1: 5%|▌ | 4/73 [00:00<00:07, 9.60it/s]
Processing PANK2--MAVS: 5%|▌ | 4/73 [00:00<00:07, 9.60it/s]
Processing PANK2--MAVS: 7%|▋ | 5/73 [00:00<00:07, 9.62it/s]
Processing WAC--SFMBT2: 7%|▋ | 5/73 [00:00<00:07, 9.62it/s]
Processing WAC--SFMBT2: 8%|▊ | 6/73 [00:00<00:06, 9.63it/s]
Processing TCF7L2--AL158212.1: 8%|▊ | 6/73 [00:00<00:06, 9.63it/s]
Processing TCF7L2--AL158212.1: 10%|▉ | 7/73 [00:00<00:06, 9.64it/s]
Processing PPL--SEC14L5: 10%|▉ | 7/73 [00:00<00:06, 9.64it/s]
Processing PPL--SEC14L5: 11%|█ | 8/73 [00:00<00:06, 9.64it/s]
Processing C18orf25--GREB1L: 11%|█ | 8/73 [00:00<00:06, 9.64it/s]
Processing C18orf25--GREB1L: 12%|█▏ | 9/73 [00:00<00:06, 9.65it/s]
Processing CENPM--PACSIN2: 12%|█▏ | 9/73 [00:00<00:06, 9.65it/s]
Processing CENPM--PACSIN2: 14%|█▎ | 10/73 [00:01<00:06, 9.65it/s]
Processing B9D1--CD82: 14%|█▎ | 10/73 [00:01<00:06, 9.65it/s]
Processing B9D1--CD82: 15%|█▌ | 11/73 [00:01<00:06, 9.65it/s]
Processing PEX3--AIG1: 15%|█▌ | 11/73 [00:01<00:06, 9.65it/s]
Processing PEX3--AIG1: 16%|█▋ | 12/73 [00:01<00:06, 9.65it/s]
Processing ZNF227--GAB2: 16%|█▋ | 12/73 [00:01<00:06, 9.65it/s]
Processing ZNF227--GAB2: 18%|█▊ | 13/73 [00:01<00:06, 9.62it/s]
Processing THAP12--ACO1: 18%|█▊ | 13/73 [00:01<00:06, 9.62it/s]
Processing THAP12--ACO1: 19%|█▉ | 14/73 [00:01<00:06, 9.63it/s]
Processing EFNA5--IKBKB: 19%|█▉ | 14/73 [00:01<00:06, 9.63it/s]
Processing EFNA5--IKBKB: 21%|██ | 15/73 [00:01<00:06, 9.63it/s]
Processing FANCA--CDK10: 21%|██ | 15/73 [00:01<00:06, 9.63it/s]
Processing FANCA--CDK10: 22%|██▏ | 16/73 [00:01<00:05, 9.64it/s]
Processing CHMP1A--FANCA: 22%|██▏ | 16/73 [00:01<00:05, 9.64it/s]
Processing CHMP1A--FANCA: 23%|██▎ | 17/73 [00:01<00:05, 9.64it/s]
Processing DDX1--AC068286.1: 23%|██▎ | 17/73 [00:01<00:05, 9.64it/s]
Processing DDX1--AC068286.1: 25%|██▍ | 18/73 [00:01<00:05, 9.65it/s]
Processing MGA--GABRB3: 25%|██▍ | 18/73 [00:01<00:05, 9.65it/s]
Processing MGA--GABRB3: 26%|██▌ | 19/73 [00:01<00:05, 9.65it/s]
Processing TLK2--AC240565.1: 26%|██▌ | 19/73 [00:01<00:05, 9.65it/s]
Processing TLK2--AC240565.1: 27%|██▋ | 20/73 [00:02<00:05, 9.65it/s]
Processing BCL2L13--EP300: 27%|██▋ | 20/73 [00:02<00:05, 9.65it/s]
Processing BCL2L13--EP300: 29%|██▉ | 21/73 [00:02<00:05, 9.65it/s]
Processing MIPOL1--TTC6: 29%|██▉ | 21/73 [00:02<00:05, 9.65it/s]
Processing MIPOL1--TTC6: 30%|███ | 22/73 [00:02<00:05, 9.65it/s]
Processing MRPS14--TNR: 30%|███ | 22/73 [00:02<00:05, 9.65it/s]
Processing MRPS14--TNR: 32%|███▏ | 23/73 [00:02<00:05, 9.65it/s]
Processing TLK2P1--AC110079.1: 32%|███▏ | 23/73 [00:02<00:05, 9.65it/s]
Processing TLK2P1--AC110079.1: 33%|███▎ | 24/73 [00:02<00:05, 9.65it/s]
Processing ATG16L2--C11orf80: 33%|███▎ | 24/73 [00:02<00:05, 9.65it/s]
Processing ATG16L2--C11orf80: 34%|███▍ | 25/73 [00:02<00:04, 9.65it/s]
Processing ZDHHC9--AL034405.1: 34%|███▍ | 25/73 [00:02<00:04, 9.65it/s]
Processing ZDHHC9--AL034405.1: 36%|███▌ | 26/73 [00:02<00:04, 9.65it/s]
Processing KDM4B--CYP4F22: 36%|███▌ | 26/73 [00:02<00:04, 9.65it/s]
Processing KDM4B--CYP4F22: 37%|███▋ | 27/73 [00:02<00:04, 9.65it/s]
Processing ANTXR2--TNFSF10: 37%|███▋ | 27/73 [00:02<00:04, 9.65it/s]
Processing ANTXR2--TNFSF10: 38%|███▊ | 28/73 [00:02<00:04, 9.65it/s]
Processing WWP2--STARD9: 38%|███▊ | 28/73 [00:02<00:04, 9.65it/s]
Processing WWP2--STARD9: 40%|███▉ | 29/73 [00:03<00:04, 9.65it/s]
Processing CASP8--STRADB: 40%|███▉ | 29/73 [00:03<00:04, 9.65it/s]
Processing CASP8--STRADB: 41%|████ | 30/73 [00:03<00:04, 9.66it/s]
Processing SPAG9--MBTD1: 41%|████ | 30/73 [00:03<00:04, 9.66it/s]
Processing SPAG9--MBTD1: 42%|████▏ | 31/73 [00:03<00:04, 9.66it/s]
Processing GOLGA6L10--GOLGA2P6: 42%|████▏ | 31/73 [00:03<00:04, 9.66it/s]
Processing GOLGA6L10--GOLGA2P6: 44%|████▍ | 32/73 [00:03<00:04, 9.66it/s]
Processing CUL4B--TMEM255A: 44%|████▍ | 32/73 [00:03<00:04, 9.66it/s]
Processing CUL4B--TMEM255A: 45%|████▌ | 33/73 [00:03<00:04, 9.66it/s]
Processing ELF2--EGFLAM: 45%|████▌ | 33/73 [00:03<00:04, 9.66it/s]
Processing ELF2--EGFLAM: 47%|████▋ | 34/73 [00:03<00:04, 9.66it/s]
Processing FN1--AC012462.2: 47%|████▋ | 34/73 [00:03<00:04, 9.66it/s]
Processing FN1--AC012462.2: 48%|████▊ | 35/73 [00:03<00:03, 9.65it/s]
Processing ANTXR1--Metazoa_SRP: 48%|████▊ | 35/73 [00:03<00:03, 9.65it/s]
Processing ANTXR1--Metazoa_SRP: 49%|████▉ | 36/73 [00:03<00:03, 9.66it/s]
Processing ANTXR1--RN7SKP168: 49%|████▉ | 36/73 [00:03<00:03, 9.66it/s]
Processing ANTXR1--RN7SKP168: 51%|█████ | 37/73 [00:03<00:03, 9.66it/s]
Processing ANTXR1--ZFYVE9P2: 51%|█████ | 37/73 [00:03<00:03, 9.66it/s]
Processing ANTXR1--ZFYVE9P2: 52%|█████▏ | 38/73 [00:03<00:03, 9.66it/s]
Processing TVP23C--CDRT4: 52%|█████▏ | 38/73 [00:03<00:03, 9.66it/s]
Processing TVP23C--CDRT4: 53%|█████▎ | 39/73 [00:04<00:03, 9.66it/s]
Processing CCNJL--FABP6: 53%|█████▎ | 39/73 [00:04<00:03, 9.66it/s]
Processing CCNJL--FABP6: 55%|█████▍ | 40/73 [00:04<00:03, 9.66it/s]
Processing SYNCRIP--SNX14: 55%|█████▍ | 40/73 [00:04<00:03, 9.66it/s]
Processing SYNCRIP--SNX14: 56%|█████▌ | 41/73 [00:04<00:03, 9.66it/s]
Processing PCDHGB2--PCDHGA8: 56%|█████▌ | 41/73 [00:04<00:03, 9.66it/s]
Processing PCDHGB2--PCDHGA8: 58%|█████▊ | 42/73 [00:04<00:03, 9.66it/s]
Processing PCDHGB2--PCDHGC5: 58%|█████▊ | 42/73 [00:04<00:03, 9.66it/s]
Processing PCDHGB2--PCDHGC5: 59%|█████▉ | 43/73 [00:04<00:03, 9.65it/s]
Processing PCDHGB2--PCDHGA11: 59%|█████▉ | 43/73 [00:04<00:03, 9.65it/s]
Processing PCDHGB2--PCDHGA11: 60%|██████ | 44/73 [00:04<00:03, 9.66it/s]
Processing PCDHGB2--PCDHGC4: 60%|██████ | 44/73 [00:04<00:03, 9.66it/s]
Processing PCDHGB2--PCDHGC4: 62%|██████▏ | 45/73 [00:04<00:02, 9.66it/s]
Processing PCDHGB2--PCDHGA10: 62%|██████▏ | 45/73 [00:04<00:02, 9.66it/s]
Processing PCDHGB2--PCDHGA10: 63%|██████▎ | 46/73 [00:04<00:02, 9.65it/s]
Processing PCDHGB2--PCDHGB6: 63%|██████▎ | 46/73 [00:04<00:02, 9.65it/s]
Processing PCDHGB2--PCDHGB6: 64%|██████▍ | 47/73 [00:04<00:02, 9.66it/s]
Processing PCDHGB2--PCDHGC3: 64%|██████▍ | 47/73 [00:04<00:02, 9.66it/s]
Processing PCDHGB2--PCDHGC3: 66%|██████▌ | 48/73 [00:04<00:02, 9.65it/s]
Processing PCDHGB2--PCDHGA9: 66%|██████▌ | 48/73 [00:04<00:02, 9.65it/s]
Processing PCDHGB2--PCDHGA9: 67%|██████▋ | 49/73 [00:05<00:02, 9.65it/s]
Processing PCDHGB2--PCDHGB7: 67%|██████▋ | 49/73 [00:05<00:02, 9.65it/s]
Processing PCDHGB2--PCDHGB7: 68%|██████▊ | 50/73 [00:05<00:02, 9.66it/s]
Processing PCDHGB2--PCDHGA12: 68%|██████▊ | 50/73 [00:05<00:02, 9.66it/s]
Processing PCDHGB2--PCDHGA12: 70%|██████▉ | 51/73 [00:05<00:02, 9.66it/s]
Processing HERC2--AC018362.1: 70%|██████▉ | 51/73 [00:05<00:02, 9.66it/s]
Processing HERC2--AC018362.1: 71%|███████ | 52/73 [00:05<00:02, 9.66it/s]
Processing HERC2--SNAP23: 71%|███████ | 52/73 [00:05<00:02, 9.66it/s]
Processing HERC2--SNAP23: 73%|███████▎ | 53/73 [00:05<00:02, 9.65it/s]
Processing RBM14--RBM4: 73%|███████▎ | 53/73 [00:05<00:02, 9.65it/s]
Processing RBM14--RBM4: 74%|███████▍ | 54/73 [00:05<00:01, 9.65it/s]
Processing CMIP--AP001970.1: 74%|███████▍ | 54/73 [00:05<00:01, 9.65it/s]
Processing CMIP--AP001970.1: 75%|███████▌ | 55/73 [00:05<00:01, 9.66it/s]
Processing CMIP--U8: 75%|███████▌ | 55/73 [00:05<00:01, 9.66it/s]
Processing CMIP--U8: 77%|███████▋ | 56/73 [00:05<00:01, 9.66it/s]
Processing HNRNPM--TIMM29: 77%|███████▋ | 56/73 [00:05<00:01, 9.66it/s]
Processing HNRNPM--TIMM29: 78%|███████▊ | 57/73 [00:05<00:01, 9.66it/s]
Processing PCDHA4--PCDHAC2: 78%|███████▊ | 57/73 [00:05<00:01, 9.66it/s]
Processing PCDHA4--PCDHAC2: 79%|███████▉ | 58/73 [00:06<00:01, 9.66it/s]
Processing PCDHA4--PCDHAC1: 79%|███████▉ | 58/73 [00:06<00:01, 9.66it/s]
Processing PCDHA4--PCDHAC1: 81%|████████ | 59/73 [00:06<00:01, 9.66it/s]
Processing PCDHA4--PCDHA13: 81%|████████ | 59/73 [00:06<00:01, 9.66it/s]
Processing PCDHA4--PCDHA13: 82%|████████▏ | 60/73 [00:06<00:01, 9.65it/s]
Processing IKBKB--CHRNA6: 82%|████████▏ | 60/73 [00:06<00:01, 9.65it/s]
Processing IKBKB--CHRNA6: 84%|████████▎ | 61/73 [00:06<00:01, 9.65it/s]
Processing IKBKB--THAP1: 84%|████████▎ | 61/73 [00:06<00:01, 9.65it/s]
Processing IKBKB--THAP1: 85%|████████▍ | 62/73 [00:06<00:01, 9.65it/s]
Processing SOGA3--KIAA0408: 85%|████████▍ | 62/73 [00:06<00:01, 9.65it/s]
Processing SOGA3--KIAA0408: 86%|████████▋ | 63/73 [00:06<00:01, 9.65it/s]
Processing TRIP10--KDM4B: 86%|████████▋ | 63/73 [00:06<00:01, 9.65it/s]
Processing TRIP10--KDM4B: 88%|████████▊ | 64/73 [00:06<00:00, 9.66it/s]
Processing CCDC169--SOHLH2: 88%|████████▊ | 64/73 [00:06<00:00, 9.66it/s]
Processing CCDC169--SOHLH2: 89%|████████▉ | 65/73 [00:06<00:00, 9.66it/s]
Processing PPIP5K1--OTUD7A: 89%|████████▉ | 65/73 [00:06<00:00, 9.66it/s]
Processing PPIP5K1--OTUD7A: 90%|█████████ | 66/73 [00:06<00:00, 9.66it/s]
Processing KLRC4--KLRK1: 90%|█████████ | 66/73 [00:06<00:00, 9.66it/s]
Processing KLRC4--KLRK1: 92%|█████████▏| 67/73 [00:06<00:00, 9.66it/s]
Processing ZNF419--ZNF772: 92%|█████████▏| 67/73 [00:06<00:00, 9.66it/s]
Processing ZNF419--ZNF772: 93%|█████████▎| 68/73 [00:07<00:00, 9.66it/s]
Processing TLK2--FAM157A: 93%|█████████▎| 68/73 [00:07<00:00, 9.66it/s]
Processing TLK2--FAM157A: 95%|█████████▍| 69/73 [00:07<00:00, 9.66it/s]
Processing ROR1--RASSF9: 95%|█████████▍| 69/73 [00:07<00:00, 9.66it/s]
Processing ROR1--RASSF9: 96%|█████████▌| 70/73 [00:07<00:00, 9.66it/s]
Processing ROR1--NTS: 96%|█████████▌| 70/73 [00:07<00:00, 9.66it/s]
Processing ROR1--NTS: 97%|█████████▋| 71/73 [00:07<00:00, 9.66it/s]
Processing RNF216--UNC93B2: 97%|█████████▋| 71/73 [00:07<00:00, 9.66it/s]
Processing RNF216--UNC93B2: 99%|█████████▊| 72/73 [00:07<00:00, 9.65it/s]
Processing CRYZL2P--SEC16B: 99%|█████████▊| 72/73 [00:07<00:00, 9.65it/s]
Processing CRYZL2P--SEC16B: 100%|██████████| 73/73 [00:07<00:00, 9.65it/s]
Processing CRYZL2P--SEC16B: 100%|██████████| 73/73 [00:07<00:00, 9.65it/s]
cat: fusion_report_db/DB-timestamp.txt: No such file or directory