SJ output too small Variant calling

[Janay Fox]

Hi,

I am trying to run  the variant calling script but am getting this  error:

EXITING because of fatal error: buffer size for SJ output is too small

Solution: increase input parameter --limitOutSJcollapsed

I have been trying to figure out a way to run the script outside of the Trinity image so that I can add + " --limitOutSJcollapsed 2000000 " which should fix this issue but I am having an issue  with pipeliner being called "Pipeliner" and I am unable to fix the script accordingly. Any suggestions?

Thanks for any help!

Best,

Janay

[Brian Haas]

Hi Janay,

 You can download the software from github (the full trinity package), modify that STAR command in 

trinityrnaseq/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py

and then just run it from there. Note, you can run this modified script through the image instead of the one that's installed directly in the image, if that makes sense.

--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/trinityrnaseq-users/fb9487a9-bc6a-4417-9637-c63a77ce0a9cn%40googlegroups.com.

--

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Janay Fox]

Oh great, running the script on the singularity image worked! Thank you so much!