Question: kinannote software installation problems
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gravatar for Elizabeth
7 months ago by
Elizabeth10
Elizabeth10 wrote:

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
kinannote • 232 views
ADD COMMENTlink modified 7 months ago by genomax63k • written 7 months ago by Elizabeth10

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.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax63k

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

ADD REPLYlink written 7 months ago by Elizabeth10

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

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax63k

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.

ADD REPLYlink modified 7 months ago by genomax63k • written 7 months ago by Elizabeth10

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?

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax63k

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

ADD REPLYlink written 7 months ago by Elizabeth10

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.

ADD REPLYlink written 7 months ago by genomax63k

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

ADD REPLYlink written 7 months ago by Elizabeth10
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