Generate structural fragments

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    • May 11, 2011 at 3:18 am #905
      Anonymous

        Hello everyone,when I run “/rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta”,I got the error follow:
        [root@localhost input]# /rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta
        Run options:
        be verbose.
        don’t run psipred.
        don’t run prof.
        don’t run jufo.
        don’t run sam.
        FILENAME: trhl2.fasta
        no id specified. parse filename instead.
        INTERMEDIATE: trhl2.fasta
        ID: trhl CHAIN: 2
        Warning: can’t find executable file /work/chu/src/shareware/psipred/bin/psipred!
        Warning: can’t find executable file /work/chu/src/shareware/psipred/bin/psipass2!
        Warning: can’t find executable file /rosetta/fragments/chemshift/pCHEMSHIFT.gnu!
        Warning: can’t find executable file /work/chu/src/shareware/jufo/molecule.exe!
        Warning: can’t find executable file /sam/bin/target99!
        Warning: can’t find executable file /sam/bin/uniqueseq!
        Warning: can’t find executable file /sam/sam.predict-2nd/!
        Warning: can’t find executable file /sam/sam.predict-2nd/predict-2nd!
        Sequence: MFIVWLWVGFAMAASVVADRSKLPPACDSMIYCHGPLLNTVQMAGLYNDSKTFVDMKIKMSPNITLEHFYDMMSRTDSNPTKADIQEFVNQNFDPEGSEFEDWRPSDWKHNPGFLAKIKDPLLHKWASALNDLWLDLGRKMKEAVKESPDLYSIIYVEHPFIVPGGRFREFYYWDSYWIIKGLLLSEMRTTAKGMVNNLLSIVDRYGFIPNGGRIYYLMRSQPPLLIPMVQLLMEDTDDLEYLREHIHTLDKEFDYWMTNHTIEVNHEGKKLKMAMYMDNSQGPRPESYKEDVDCARHFDTTEKKEELYAELKAAAESGWDFSSRWFILNGTNKGNLTNLKVRSIIPVDLNAILCWNAQLMMEYHTRLQNEEKASYYRRIHDDFMEAIEELLWHEDVGVWLDYSLESSRRRDYFYPSNLSPLWAGSYDKARKDYFVNRVVNYLDKVKMDIFEGGIPTTFEHTGEQWDYPNAWPPLQYIVIMGLANTGHPEAMRYATELATKWVRSNFEVWKQKAAMLEKYDATILGGLGGGGEYVVQTGFGWSNGVVMSLLNRYGDVISAADNFGTAAESGAVYGAGVGAGGVVTALLVVLASLAAGTLGLMVYKRRKDYAGFCNGEVDKLISKKPYTELKSLNGASNQKQR
        cmd is: /blast/bin/blastpgp -t T -i trhl2.fasta -F F -j2 -o trhl2.blast -d /blast/db/nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C trhl2.check -Q trhl2.pssm
        [blastpgp] WARNING: a standard checkpoint file should have extension “.chk”.

        cmd is: /blast/bin/blastpgp -t T -i trhl2.fasta -F F -j2 -o trhl2.blast -d /blast/db/nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C trhl2.check -Q trhl2.pssm
        [blastpgp] WARNING: a standard checkpoint file should have extension “.chk”.

        checkpoint psi-blast failed!

      • May 24, 2011 at 5:48 pm #5632
        Anonymous

          You will need to use at least two secondary structure predictions for fragment generation to make sense, but that’s not the problem here. It seems that blast is failing. Try running the blast command directly to get a better idea of what’s going on. That is, type

          /blast/bin/blastpgp -t T -i trhl2.fasta -F F -j2 -o trhl2.blast -d /blast/db/nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C trhl2.check -Q trhl2.pssm

          If this fails, check the paths for the blastpgp executable and the nr database and update make_fragments.pl as necessary.

        • June 6, 2012 at 6:54 pm #7185
          Anonymous

            I’m running the same script on Ubuntu and ran into the same error. I found that the make_fragment.pl script was looking for checkpoint files with a .check extension rather than a .chk extension… I’m not sure what the difference is between them or even if the make_fragments.pl script included in the Rosetta 3.4 release is correct. Has anyone run make_fragments.pl successfully recently? If so, what tools did you install, how much customization was necessary to get it running?

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