error running “helix_preassemble_setup.py”

[Anonymous]

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__

    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

---

Is there any solution for that.

Thanks.

[Anonymous]

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.

[Author]

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