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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Blast runtime error in computing comparative metrics #82

Closed hyundoo closed 9 years ago

hyundoo commented 10 years ago

When I try to run transrate to compute the reference based metrics i am getting a Blast runtime error. I tried to then compute this set of metrics on the sample data provided using the following command:

transrate --assembly assembly.fasta --reference Os.protein.fa

(sample data is downloaded from: https://github.com/Blahah/transrate/tree/master/test/data)

I get the following error (the same error that I am getting on my own data set): ../Transrate/0.3.1/gems/crb-blast-0.4.0/lib/crb-blast/crb-blast.rb:232:in block in run_blast_with_splitting': BLAST Error: (RuntimeError) from ../Transrate/0.3.1/gems/threach-0.2.0/lib/threach.rb:15:incall' from ../Transrate/0.3.1/gems/threach-0.2.0/lib/threach.rb:15:in `block (2 levels) in threach'

Could you please help me in figuring out what I am doing wrong. Thanks.

blahah commented 10 years ago

Please could you tell us your ruby version?

Run:

$ ruby --version
hyundoo commented 10 years ago

The ruby version I have is:

$ ruby --version ruby 2.1.2p95 (2014-05-08 revision 45877) [x86_64-linux]

cboursnell commented 10 years ago

Hi Hyundoo, I believe this is an error caused by the gem 'crb-blast' that is a dependency of transrate. Before running blast, the crb-blast gem splits the input into separate fasta sequences to achieve better parallelisation. The problem was that there were more threads specified than fasta sequences so that some of the smaller fasta files were empty causing blast to crash. This problem has been fixed in crb-blast. If you run gem uninstall crb-blast and then gem install crb-blast this should get the latest version and transrate should use this. Please let us know if you are having any further problems, Cheers, Chris.