ab inito memberane(error in alignblast.pl)

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    • May 4, 2011 at 6:41 am #897
      Anonymous

        Hello everyone:
        When I run “/rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl t2.fasta t2.span /rosetta/blast/bin/blastpgp /rosetta/nr /rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl”,I got the error that:
        [root@localhost input]# /rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl t2.fasta t2.span /rosetta/blast/bin/blastpgp /rosetta/nr /rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl
        Error in alignblast.pl: blast output file t2.blast truncated:
        readline() on closed filehandle MSA at /rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl line 91.
        2 0 0

      • May 6, 2011 at 8:52 am #5543
        Anonymous

          Who can help me,I am very anxiety，I can’t solve the error.Even if I re-download the db include nr00,nr01,nr02,nr03,nr04,nr05,I decompress them and put them into nr directory,I run “/rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl t2.fasta t2.span /blast/bin/blastpgp /blast/nr /rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl”,it just like running,but I also got the error:
          [root@localhost input]# /rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl t2.fasta t2.span /blast/bin/blastpgp /blast/nr /rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl
          Running:
          /blast/bin/blastpgp -i t2.fasta -d /blast/nr -j 2 -h 0.001 -b5000 -v5000 -o t2.blast
          Error in alignblast.pl: blast output file t2.blast truncated:
          readline() on closed filehandle MSA at /rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl line 91.
          2 0 0

        • May 6, 2011 at 6:30 pm #5544
          Anonymous

            I have no familiarity with membrane ab initio, so I’m completely guessing here, but it looks like your blast is failing somehow.

            See if you can run the printed command (“/blast/bin/blastpgp -i t2.fasta -d /blast/nr -j 2 -h 0.001 -b5000 -v5000 -o t2.blast”) by itself and see what happens. Take a look at the t2.blast output file and see if it looks like it’s supposed to.

            Also, I found these posts which may be some help:
            http://www.rosettacommons.org/node/1751
            http://www.rosettacommons.org/node/2298

          • May 8, 2012 at 12:10 pm #7087
            Anonymous

              Please see my reply to
              http://www.rosettacommons.org/content/membrane-folding-blastpgp-error

            • June 8, 2012 at 2:09 pm #7193
              Anonymous

                I am also getting the same error Error in alignblast.pl: blast output file filename.fasta.out truncated. readline () on closed filehandle MSA at ./run_lips.pl line 92.

                Any one got solution for this error?

              • May 10, 2011 at 3:08 am #5554
                Anonymous

                  Hi rmoretti,thank you for your reply,I have read them,but I can’solve the error.Do you have a new solution.

                • May 10, 2011 at 3:25 am #5556
                  Anonymous

                    Thank you for the tips, I accidentally solved the problem.

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