Dear Rosetta users,
I recently install Rosetta and want to work with Rna_Denovo, when I run the command line below I got this error:
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$RNA_TOOLS/bin/helix_preassemble_setup.py -secstruct secstrcut -fasta fasta
.((((((((......((((((....)))))).(((...((((.....))))..)))........))))))))........(((((......((((((...)))))).(((...((((....((((....)))).....))))..))).......)))))
Traceback (most recent call last):
File "/rosetta/2020-10/tools/rna_tools//bin/helix_preassemble_setup.py", line 107, in <module>
subprocess.check_call([str(elem) for elem in cmdline.split()])
File "/usr/lib64/python2.7/subprocess.py", line 537, in check_call
retcode = call(*popenargs, **kwargs)
File "/usr/lib64/python2.7/subprocess.py", line 524, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
errread, errwrite)
File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
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Is there any solution for that.
Thanks.
I'm guessing the issue is that the helix_preassemble_setup.py at line 75 is asking for the `rna_denovo` application. There's two potential issues here. The first is that the rosetta/source/bin directory may not be in your path. The other is likely that you don't have a plain `rna_denovo` application -- you may have an `rna_denovo.default.linuxgccrelease` application, but not a `rna_denovo` application.
If you fixed those issues (e.g. by putting a symlink in your path called `rna_denovo` which points to the appropriate rna_denovo application in your rosetta/source/bin directory), then I think it would fix this issue.