A problem with “make_fragments.pl” script dependencies

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    • August 16, 2019 at 11:30 am #3221
      Anonymous

        Dear fellows,

        I would like to generate fragments for protein sequence structure prediction ab initio locally, on my laptop, without involving any server, such as Robetta. I carry out it with a help of make_fragments.pl script. And I met with several problems with make_fragment.pl dependencies. I want to solve these problems. Could you advise me, if you can, how to solve them, please?

        My first problem consists in follows:

        Firstly, during run such bash-terminal command “~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/make_fragments.pl name.fasta >& make_fragments.local” install_dependencies.pl script couldn’t install all necessary dependencies, or install it incorrectly. For example, it can not install correctly psipred:

        “Can’t exec “make”: No such file or directory at ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/install_dependencies.pl line 138.

        Can’t exec “make”: No such file or directory at ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/install_dependencies.pl line 144.

        ERROR! psipred installation failed!”

        Should I (re)install these dependencies on ~/fragment_tools directory on my own through bash-terminal?

        Other problem consists in next:

        “WARNING! ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/../../main/source/bin/fragment_picker.boost_thread.linuxgccrelease does not exist. Trying default.

        ERROR! ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/../../main/source/bin/fragment_picker.default.linuxgccrelease does not exist.”

        I downloaded such version of Rosetta with binaries, where all default.scripts are replaced by static.scripts. It means, that I should replace “fragment_picker.default.linuxgccrelease” to “fragment_picker.static.linuxgccrelease”, in “make_fragments.pl” script, shouldn’t I?

        For better clarity I attach make_fragments_local.pdf (log-file, where all problems and features are displayed) and a screenshot of ~/fragment_tools directory.

        I will be sincerely grateful for your response and help and I am looking forward to it.

        Best regards,

        Corvin.

      • August 18, 2019 at 10:25 pm #14880
        Anonymous 

          
Can't exec "make": No such file or directory at ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/install_dependencies.pl line 144.

          it looks like you’re missing ‘make’

          it looks like you’re using linux.

           

          so run the command: 


          
sudo apt-get install make -y

           

        • August 27, 2019 at 7:46 am #14913
          Anonymous

            Dear danpf,

            I am really thankful for your response and sorry for my slow reply.

            I fixed that problem with make, but I met with such problems:

            “Resolving http://www.ncbi.nlm.nih.gov (www.ncbi.nlm.nih.gov)… 130.14.29.110, 2607:f220:41e:4290::110

            Connecting to http://www.ncbi.nlm.nih.gov (www.ncbi.nlm.nih.gov)|130.14.29.110|:80… connected.

            HTTP request sent, awaiting response… 301 Moved Permanently

            Location: https://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl [following]
            –2019-08-26 12:52:03– https://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl

            Connecting to http://www.ncbi.nlm.nih.gov (www.ncbi.nlm.nih.gov)|130.14.29.110|:443… connected.

            HTTP request sent, awaiting response… 404 Not Found

            2019-08-26 12:52:03 ERROR 404: Not Found.

            ERROR! wget http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl failed.

            WARNING!
            ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/../../main/source/bin/fragment_picker.boost_thread.linuxgccrelease does not exist. Trying default.
            ERROR! ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/../../main/source/bin/fragment_picker.default.linuxgccrelease does not exist.”

            How I understood, there are problems about foregoing sites. It is looked like, that these sites are expired, or don’t exist more. How I can fix these problems with these sites?

            Regards,

            Corvin.

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