ab inito memberane error

[Anonymous]

I’ve got an error while I am running the following command:

/soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abi nitio/run_lips.pl test.ali test.span /usr/bin/blastp /home/albert/softbake/biosoft/rosettadb/nrdb /soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abinitio/ alignblast.pl

error:
Error in alignblast.pl: blast output file test.ali truncated:
readline() on closed filehandle MSA at /soft/rosetta-3.2/rosetta_source/src/ap ps/public/membrane_abinitio/run_lips.pl line 91.

could you please tell me how to solve this?

THX

[Anonymous]

Hi,

You need to use blastpgp (not blastp) program (see the membrane_abinitio documentation) – it is a part of Legacy Blast package that you can download from:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/
here is description of the package:
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html#7

[Anonymous]

Your problem is actually not related to membrane ab initio protocol. You need to follow the documentation carefully – it says that you should specify “path to nr database” – /home/albert/install/rosetta-3.2/blast-db in your command line is not a correct path – correct path should look like “/scratch/shared/genomes/nr” (see documentation) – with “nr” at the end – not “blast-db”. Blast nr database contains many files, but they all begin with “nr”. Always pay attention to error and/or warning messages that you are getting – you could have figured out the source of the problem if you’ve tested blastpgp program by itself and if you’ve read the warning in your log: [blastpgp] WARNING: Unable to open blast-db.pin

[Anonymous]

THX for kind reply.
I renamed the folder to “nr” and run it again, it works now but there are still many wanning messages:

/home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl test.fasta test.span /home/albert/install/rosetta-3.2/blast-2.2.24/bin/blastpgp /home/albert/install/rosetta-3.2/nr /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/alignblast.pl
Running:
/home/albert/install/rosetta-3.2/blast-2.2.24/bin/blastpgp -i test.fasta -d /home/albert/install/rosetta-3.2/nr -j 2 -h 0.001 -b5000 -v5000 -o test.blast
[blastpgp] WARNING: Unable to open nr.pin
[blastpgp] WARNING: Unable to open nr.pin
[blastpgp] WARNING: [000.000] Unable to open nr.pin
Can’t exec “/bin/sh”: Argument list too long at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 127.
Use of uninitialized value $data in print at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 129.
Use of uninitialized value $data in split at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 165.
Use of uninitialized value within @resnum in array dereference at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 201.
Use of uninitialized value within @resnum in array dereference at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 202.
Use of uninitialized value within @resnum in array dereference at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 206.
Use of uninitialized value within @resnum in array dereference at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 206.
Use of uninitialized value within @resnum in array dereference at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 206.
Use of uninitialized value within @resnum in array dereference at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 206.
Use of uninitialized value within @resnum in array dereference at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 206.
Use of uninitialized value within @resnum in array dereference at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 206.
Use of uninitialized value within @resnum in array dereference at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/run_lips.pl line 206.
3 5 5
5 3 2
0 2 2
0 5 5
4 6 6
2 4 4

[Anonymous]

[Anonymous]

THX for kind reply.
It is still doesn’t work. Moreover, I found a test.blast in the directory, but it is empty…. and here is my log file:

---

Desktop/test> /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio//run_lips.pl test.fasta test.span /home/albert/install/rosetta-3.2/blast-2.2.24/bin/blastpgp /home/albert/install/rosetta-3.2/blast-db /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio/alignblast.pl

Running:
/home/albert/install/rosetta-3.2/blast-2.2.24/bin/blastpgp -i test.fasta -d /home/albert/install/rosetta-3.2/blast-db -j 2 -h 0.001 -b5000 -v5000 -o test.blast
[blastpgp] WARNING: Unable to open blast-db.pin
[blastpgp] WARNING: Unable to open blast-db.pin
Error in alignblast.pl: blast output file test.blast truncated:
readline() on closed filehandle MSA at /home/albert/install/rosetta-3.2/source/src/apps/public/membrane_abinitio//run_lips.pl line 91.
4 2 2
5 0 0
3 5 5
0 5 5
6 4 4
4 2 2
2 4 4

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