I have use the following command:
/rosetta31/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl 1s_.fasta 1s.span /bin/blastpgp database/nr rce/src/apps/public/membrane_abinitio/alignblast.pl
but it shows:
Error in alignblast.pl: blast output file 1s_.blast truncated:
readline() on closed filehandle MSA at /rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl line 91.
what does this mean?
You may have got this problem sorted by now, but I've had the same thing so I thought I'd write anyway.
The error message that you're getting means that the msa file that run_lips.pl is trying to read in line 91 has not been opened and thus can't be read. In my case this was because creation of the msa file, which is supposed to happen in lines 81-84 of run_lips.pl, wasn't occuring, so the msa file that run_lips.pl is trying to open simply doesn't exist. As line 83 of run_lips.pl details, the msa file is created by running the script alignblast.pl on a blast file that is made on lines 74-79 of run_lips.pl.
In my case, the problem was that the blast file wasn't being created. I eventually realised this was because of problems with the nr database: first of all, I hadn't formatted it and also, I think the database files need to be in the working directory - that is certainly what made things work for me in the end.
> I have use the following command:
> /rosetta31/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl 1s_.fasta 1s.span /bin/blastpgp database/nr rce/src/apps/public/membrane_abinitio/alignblast.pl
> but it shows:
> Error in alignblast.pl: blast output file 1s_.blast truncated:
> readline() on closed filehandle MSA at /rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl line 91.
> what does this mean?
I see that trouble with this command has come up a few times, but I am currently having trouble with it as well and haven't found an answer in these posts.
I see the creation of an empty .blast file when I run run_lips, but I cannot figure out what is causing the problem. The command I'm using is:
rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl mgrB.fasta mgrB.span /Applications/blast-2.2.25/bin/blastpgp /Applications/blast-2.2.25/data/nr rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl
and my error message is:
Error in alignblast.pl: blast output file mgrB.blast truncated:
readline() on closed filehandle MSA at rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl line 91.
0 2 2
The mystifying thing is that if I just run the command:
/Applications/blast-2.2.25/bin/blastpgp -i mgrB.fasta -d /Applications/blast-2.2.25/data/nr -j 2 -h 0.001 -b5000 -v5000 -o mgrB.blast
which is lifted straight out of the code for run_lips.pl, I get a perfectly normal/valid output file. It's almost as if run_lips.pl isn't waiting for the completion of the blast search before attempting to run alignblast.pl. I'm still learning how to navigate the world of command line interfaces, so perhaps there's just something simple here that I need to adjust to make this run smoothly. Any advice?
Please see my reply to