kinannote software installation problems

Question

[Elizabeth]

Hello All, I am trying to install Kinannote (for eukaryotic kinase annotation from proteome) in my system, but even though the installation message says "successful", the results for the test run is just a bunch of zeros. I have read the manual a dozen times, and tried re-installing the software, but the result is the same everytime. Has anyone faced a similar situation while using Kinannote ? The dependencies to run Kinannote are hmmsearch from HMMER and blastall. I have noticed, it says "no such file or directory" for blastall, but the files exists. I am not sure what is going wrong or if anyone has any suggestions for other tools I could use to annotate the kinases in my proteome, please advice.

Running Kinannote_1.0.pl on spombe.fasta.
The resulting draft kinome should be ready in about 5 minutes.

Searching spombe.fasta with discovery.hmm...
Scoring 0 candidate kinases using Pkinase_scoring_matrix.discTrans...
BLASTing  candidate kinases against KDB_20111223b...
**nice: ‘/home/ncbi blast//blastall’: No such file or directory**
Parsing BLAST output...
Applying cutoffs to identify and classify protein kinases...

Kinannote did not detect any protein kinases in the input file spombe.fasta!


Done!

The number of uniquely-identified sequences in spombe.fasta is 5142
The number of ePKs in spombe.fasta is 0: ePKs comprise 0.000 % of this proteome
The fraction of core ePK families found in this proteome is 0.000 (1 is best)
A list of hits with standardized names may be found in spombe.names
A summary of this kinannote run may be found in spombe.run_summary

[GenoMax]

If that files exists then the space in the directory name (Please never use spaces in unix file/directory names) may be causing this issue. Did you select that name or did the program install do that automatically? You could try renaming the directory (replace the space with an _) and then try adding it to your $PATH to see if that fixes the problem.

[Elizabeth]

Thank you. I did that, but it still displays the same error.

[GenoMax]

Are you able to run blastall -help and see command help output or do you get an error?

[Elizabeth]

This is what I get when I type blastall

blastall 2.2.26   arguments:

  -p  Program Name [String]
  -d  Database [String]
    default = nr
  -i  Query File [File In]
    default = stdin
  -e  Expectation value (E) [Real]
    default = 10.0

Output truncated to save space: @genomax.

[GenoMax]

That all looks good. So legacy blast is properly installed and working (this requires old blast correct?).

So the problem is somewhere in kinannote. Is that a script or a compiled program? Can you take a look to see if you can change the location of blastall appropriately in kinannote?

[Elizabeth]

Yes, It's exactly the same output as mine.

[GenoMax]

Did you run setup_Kinannote.pl again since you changed the name of that directory?

If appropriate versions of blastall and hmmsearch are not found, locate or install them, rerun setup_Kinannote.pl and provide paths to them at the appropriate prompts.

[Elizabeth]

Kinannote is still not working. I reinstalled the software, but it keeps giving the same result after the test run.