Error while running “make_fragments.pl”…..[blastpgp] ERROR: Arguments must start with ‘-‘

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    • November 3, 2011 at 8:25 am #1074
      Anonymous

        hello

        I am encountering errors while trying to make fragments locally by using the script “make_fragments.pl”. The command which I am using is

        perl make_fragments.pl -verbose -nosam -noporter 1elwA.fasta

        but it gives error

        VERBOSE.
        don't run porter.
        don't run sam.
        FILENAME: 1elwA.fasta
        no id specified. parse filename instead.
        INTERMEDIATE: 1elwA.fasta
        ID: 1elw CHAIN: A
        Sequence: EQVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEAR
        cmd is: /home/ammarah/Documents/blast-2.2.25/bin/blastpgp -a 1 -t 1 -i 1elwA.fasta -F F -j2 -o 1elwA.nr.blast -d /home/ammarah/Documents/blast-2.2.25/db/nrfilt.00 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.01 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.02 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.03 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.04 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.05 -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C 1elwA.nr.chk -Q 1elwA.nr.pssm
        [blastpgp] ERROR: Arguments must start with '-' (the offending argument #14 was: '/home/ammarah/Documents/blast-2.2.25/db/nrfilt.01')
        cmd is: /home/ammarah/Documents/blast-2.2.25/bin/blastpgp -a 1 -t 1 -i 1elwA.fasta -F F -j2 -o 1elwA.nr.blast -d /home/ammarah/Documents/blast-2.2.25/db/nrfilt.00 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.01 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.02 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.03 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.04 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.05 -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C 1elwA.nr.chk -Q 1elwA.nr.pssm
        [blastpgp] ERROR: Arguments must start with '-' (the offending argument #14 was: '/home/ammarah/Documents/blast-2.2.25/db/nrfilt.01')
        checkpoint psi-blast failed!

        Just in case its important, my .ncbirc file has the following lines

        [NCBI]
        DATA= /home/ammarah/Documents/blast-2.2.25/data
        [BLAST]
        BLASTDB=/home/ammarah/Documents/blast-2.2.25/db/nrfilt.00 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.01 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.02 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.03 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.04 /home/ammarah/Documents/blast-2.2.25/db/nrfilt.05

        Can anyone please help me out with this error?? :(

      • November 3, 2011 at 6:22 pm #6214
        Anonymous

          I would guess that you have a line break (an enter mark) before the nrfilt.05 path, so it is being interpreted improperly by the program.

          In general, nobody (at least nobody on these boards) is competent to discuss make_fragments.pl any longer; there should be a version of fragment generation included as an application within Rosetta 3.3 (should be a demo for it in the demos).

        • March 12, 2012 at 8:43 pm #6802
          Anonymous

            Try changing the $NR and $FILTNR variables in make_fragments.pl to just the base name without any numbers
            i.e.

            my $NR = "/home/ammarah/Documents/blast-2.2.25/db/nr"; # nr blast database filename
            my $FILTNR = "/home/ammarah/Documents/blast-2.2.25/db/filtnr"; # filtnr blast database filename

          • November 4, 2011 at 9:14 am #6219
            Anonymous

              Thanks smlewis for the reply.

              Actually I have rosetta3.3 installed but the problem is that I want to use make_fragment.pl to generate fragments instead of fragment_picker.linuuxgccrelease. I have searched for the error (http://old.nabble.com/error-in-run-blastpgp-td30586352.html , http://lists.osc.edu/pipermail/mpiexec/2009/001069.html) and found that the error is due to some sort of syntax error in quotes or as you said due to the line break. I have tried removing the spaces between the path in make_fragment.pl script but its still of no use. The error is still the same. Any thoughts?? I shall be very thankful for it.

            • November 4, 2011 at 2:58 pm #6220
              Anonymous

                To repeat: I have no idea how to use make_fragments.pl (or blastpgp). I’m throwing out wild guesses here.

                Maybe the -d option won’t take more than one argument and it’s upset that you are giving it 5. Is there a way to combine the arguments into one file? Or give it a folder path instead of a file path?

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