error running “helix_preassemble_setup.py”

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    • November 3, 2020 at 9:54 am #3617
      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.

      • February 9, 2021 at 8:19 pm #15733
        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.

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