Transcriptome assembly evaluation with transrate

Question

[Carlos Caicedo]

Dear all

I am having a problem using the software Transrate to perform the transcriptome assembly evaluation. I get this message after I try to run the software.

   usuario@FINGNVO18-228CC:~$ transrate --assembly
    ./example_data/transcripts.fa --left ./example_data/left.fq --right
    ./example_data/right.fq --output ./tutorial2

    Dependencies are missing:

     -salmon (0.6.0)

    You are running the packaged version of transrate

    This comes with the read-metrics dependencies pre-installed

But, before I try to run the programm I checked the packages installed.

usuario@FINGNVO18-228CC:~$ transrate --install-deps ref
Checking dependencies
All dependencies installed

I would be very thankful if someone can help me.

Regards

Carlos

[Medhat]

can you run transrate --install-deps all

or ues transrate --help

see If you can install salmon

[Carlos Caicedo]

When I run transrate --install-deps all

I get this message:

usuario@FINGNVO18-228CC:~$ transrate --install-deps all
[ERROR] 2017-02-08 15:22:39 : install-deps all is not valid. You must specify one of: ref

And, when I run

usuario@FINGNVO18-228CC:~$ transrate --install-deps ref
Checking dependencies
All dependencies installed

That means, salmon dependencie is installed, but when I run the program appear the message mentioned before.

[Sej Modha]

Did you try running the pre-built linux executables that are available to download from http://hibberdlab.com/transrate/installation.html?

[Carlos Caicedo]

Yes, I did. I was running the tutorial $ transrate --assembly transcripts.fa It worked well.

But, when I tried to run

$ transrate --assembly transcripts.fa \
  --left left.fq \
  --right right.fq

It did not executed.

[Emily Wasson]

Has this issue been resolved yet? I am facing the same problem

[Carlos Caicedo]

I found the solution here.

Some people solved this problem deleting the file librt.so.1

Just in case, I renamed that one library and worked the problem out.