EXITING because of FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem

[sukhmanpreet33]

Hi,
I was trying to generate starindex and got the following error:
EXITING because of FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem

I did convert the gff file to gtf format using gffread and everything seemed okay. Here are the star parameters that I used:
STAR --runThreadN 32
--runMode genomeGenerate
--genomeDir ${STAR_INDEX_DIR}
--genomeFastaFiles ${GENOME_DIR}/GWHBHPU00000000.genome.fasta
--sjdbGTFfile ${GENOME_DIR}/GWHBHPU00000000.gtf
--sjdbOverhang 139

Here is a tail of the log file:
Apr 01 12:08:20 Finished preparing junctions
Apr 01 12:08:20 ..... inserting junctions into the genome indices
Apr 01 12:08:37 Finished SA search: number of new junctions=154115, old junctions=0
Apr 01 12:09:02 Finished sorting SA indicesL nInd=85687584

EXITING because of FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem
SOLUTION: please contact STAR author at https://groups.google.com/forum/#!forum/rna-star

Apr 01 12:09:02 ...... FATAL ERROR, exiting

Thanks,
Sukhman

[Alexander Dobin]

Hi @sukhmanpreet33

Please use the latest version of STAR - if it does not help, please post your Log.out file.