Reply To: membrane modeling error!

[Anonymous]

Hi,

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?