QuestionsCategory: Select a CategoryTrouble building CTAT custom genome
mannheimerjd@nih.gov asked 6 days ago

Hi, I am looking into gene fusions in several canine tumors and plan on using STAR FUSION. As I understand first I need to build a CRTA genome. I have been following https://github.com/NCIP/ctat-genome-lib-builder/wiki as a resource but have been unable to get it to run. I keep on getting a error
“died with ret 9 No such file or directory at /data/mannheimerjd/sfusion/ctat-genome-lib-builder/lib.Pipeliner line 186”
In the code preceding the error message it seems to be trying to find my GTF file. However, the GTF file is in the current working directory and I do not understand why it cannot find it. 
any help would be much appreciated. 

1 Answers
stonelakeak@nih.gov Staff answered 6 days ago

Hi Josh,
I looked at the GitHub resource you have mentioned for NCIP/CTAT.
I’ve noticed there is an active user community for this resource at
https://groups.google.com/forum/#!forum/trinity_ctat_users

I point that out because that may be the most direct way to get your question answered.

If you’d like us to help you sort out the problem, we can also try that but it will be a bit involved – we will need the exact command lines you are using and take a look at your user directories and may have to do an install myself of the software and libraries to help track down the problem.

How much experience do you have working at the unix command line? Is this a new effort for you or something you’ve done a lot of?

So, for now – I suggest you try the user trinity_ctat_users forum first. Let me know how that goes and if you need more help from us here at BTEP. You can send further questions in to ncibtep@nih.gov, that will come directly to us.