# error running "helix_preassemble_setup.py"

2 posts / 0 new
error running "helix_preassemble_setup.py"
#1

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:

------------------------------------------------------------------------------------------------------------------------------------------------

\$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__
File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
------------------------------------------------------------------------------------------------------------------------------------------------

Is there any solution for that.

Thanks.

Category:
Post Situation:
Tue, 2020-11-03 01:54
zahra_AZ

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.

Tue, 2021-02-09 12:19
rmoretti