getting a3m files

[Anonymous]

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

 

[Anonymous]

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

[Anonymous]

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

[Author]

Posts