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ab inito memberane(error in alignblast.pl)

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ab inito memberane(error in alignblast.pl)
#1

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

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Tue, 2011-05-03 23:41
kingljy

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

Fri, 2011-05-06 01:52
kingljy

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

Fri, 2011-05-06 11:30
rmoretti

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

Mon, 2011-05-09 20:08
kingljy

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

Mon, 2011-05-09 20:25
kingljy
Tue, 2012-05-08 05:10
arthuc01

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?

Fri, 2012-06-08 07:09
karthishanmugam