Dear author,
I am running the command: hyphy relax --alignment /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/07.deletestopcodon/evm.model.ptg000001l.100.fa --tree /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/00.tree/evm.model.ptg000001l.100.phy.treefile.mark --test FG2 --reference FG1 --output /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/01.relax.out/evm.model.ptg000001l.100.json > /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/01.relax.out/evm.model.ptg000001l.100.relax.log 2>&1;
My tree : (Fan{FG1},((((((((Hcr,Cgu),(Tsw,Pty)),Hgl{FG1}),(Gca{FG2},Bsu{FG2})),Cho{FG1}),Fme{FG1}),Fda{FG1}),Fdm{FG1}),Fmi{FG1});
My alignment file:
However, I only got the log file but can not generate the json file. The log file looks like normal and is attached.
evm.model.ptg000001l.100.relax.log
Could you give me any suggestions?
Looking forward with your reply.
Best wishes,
Na Wan
Dear author, I am running the command:
However, I only got the log file but can not generate the json file. The log file looks like normal and is attached.
evm.model.ptg000001l.100.relax.log
Could you give me any suggestions?
Looking forward with your reply.
Best wishes,
Na Wan
hyphy relax --alignment /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/07.deletestopcodon/evm.model.ptg000001l.100.fa --tree /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/00.tree/evm.model.ptg000001l.100.phy.treefile.mark --test FG2 --reference FG1 --output /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/01.relax.out/evm.model.ptg000001l.100.json > /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/01.relax.out/evm.model.ptg000001l.100.relax.log 2>&1; My tree :(Fan{FG1},((((((((Hcr,Cgu),(Tsw,Pty)),Hgl{FG1}),(Gca{FG2},Bsu{FG2})),Cho{FG1}),Fme{FG1}),Fda{FG1}),Fdm{FG1}),Fmi{FG1});My alignment file: