ab inito memberane error – Rosetta Commons

This topic has 5 replies, 2 voices, and was last updated 13 years, 10 months ago by Anonymous.

Viewing 4 reply threads

Author

Posts
- February 14, 2011 at 6:58 pm #786
  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
- February 14, 2011 at 9:02 pm #5022
  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
- February 16, 2011 at 2:13 am #5033
  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
- February 16, 2011 at 9:10 am #5036
  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
- February 16, 2011 at 2:46 pm #5037
  Anonymous
- February 15, 2011 at 8:26 pm #5027
  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
Author

Posts

Viewing 4 reply threads

You must be logged in to reply to this topic.