Hi,
I am using STAR-2.6.0a for custom genome index and paired end reads and getting following error:

EXITING because of fatal error: buffer size for SJ output is too small
Solution: increase input parameter --limitOutSJcollapsed
Aug 23 08:37:22 ...... FATAL ERROR, exiting

options I used:
--genomeLoad NoSharedMemory --genomeDir --runThread 1 --readFilesIn --outSAMtype BAM Unsorted --limitOutSJcollapsed int>0 --outFileNamePrefix

same error with and without using this flag : --limitOutSJcollapsed int>0