Hi,
I want to use RoseTTAfold on the Robetta.new server but it requires an a3m file I dont know how to generate.
I saw a script on the github page (https://github.com/RosettaCommons/RoseTTAFold/blob/main/input_prep/make_msa.sh) that to my understanding is supposed to convert fasta to a3m but it dosent seem to work and I get the following error:
/var/spool/slurmd/job584522/slurm_script: line 28: hhblits: command not found
/var/spool/slurmd/job584522/slurm_script: line 29: hhfilter: command not found
/var/spool/slurmd/job584522/slurm_script: line 30: hhfilter: command not found
grep: L2_m3a/hhblits/t000_.1e-30.id90cov75.a3m: No such file or directory
grep: L2_m3a/hhblits/t000_.1e-30.id90cov50.a3m: No such file or directory
1e-10
/var/spool/slurmd/job584522/slurm_script: line 28: hhblits: command not found
/var/spool/slurmd/job584522/slurm_script: line 29: hhfilter: command not found
/var/spool/slurmd/job584522/slurm_script: line 30: hhfilter: command not found
grep: L2_m3a/hhblits/t000_.1e-10.id90cov75.a3m: No such file or directory
grep: L2_m3a/hhblits/t000_.1e-10.id90cov50.a3m: No such file or directory
1e-6
/var/spool/slurmd/job584522/slurm_script: line 28: hhblits: command not found
/var/spool/slurmd/job584522/slurm_script: line 29: hhfilter: command not found
/var/spool/slurmd/job584522/slurm_script: line 30: hhfilter: command not found
grep: L2_m3a/hhblits/t000_.1e-6.id90cov75.a3m: No such file or directory
grep: L2_m3a/hhblits/t000_.1e-6.id90cov50.a3m: No such file or directory
1e-3
/var/spool/slurmd/job584522/slurm_script: line 28: hhblits: command not found
/var/spool/slurmd/job584522/slurm_script: line 29: hhfilter: command not found
/var/spool/slurmd/job584522/slurm_script: line 30: hhfilter: command not found
grep: L2_m3a/hhblits/t000_.1e-3.id90cov75.a3m: No such file or directory
grep: L2_m3a/hhblits/t000_.1e-3.id90cov50.a3m: No such file or directory
cp: cannot stat 'L2_m3a/hhblits/t000_.1e-3.id90cov50.a3m': No such file or directory
did anyone encounter this problem?
thanks,
Alon
In this case it looks like it can't find hhblits & hhfilter. You can get them by installing hhsuite https://github.com/soedinglab/hh-suite and having it in your path when running the script
Thank you!
after installing I still had some problems but I found this site: https://toolkit.tuebingen.mpg.de/ that can generate a3m files and generaly do hhsuit stuff online.
Alon