cannot insert junctions on the fly because of strand GstrandBit problem

[Analeigh Gui]

Dear Alex,

Thanks for your great effort maintaining STAR.

I encountered the error "cannot insert junctions on the fly because of strand GstrandBit problem" when working on plant (Hv_Morex) genome. I also added the genome of phiX to see if there is any phiX contamination.

command:

STAR --runMode genomeGenerate --runThreadN 10 --genomeDir pgsb --genomeFastaFiles Hv_Morex.pgsb.Jul2020.fa phix.fa --sjdbGTFfile head.gtf --sjdbOverhang 100

version: 2.5.2b (I cannot change the version, because the analysis pipeline requires this particular version of STAR)

gtf attached: It's converted from gff3, and I took the first few lines for dummy run. The original gff3 doesn't have gene_id and transcript_id, so I manually added these two entries.

Log.out attached: Below is the end of the file.

Processing sjdbGTFfile=head.gtf, found:
                3 transcripts
                4 exons (non-collapsed)
                1 collapsed junctions
Jan 25 20:29:14 ..... finished GTF processing
Jan 25 20:29:14   Loaded database junctions from the GTF file: head.gtf: 1 total junctions

Jan 25 20:29:14   Finished preparing junctions
Jan 25 20:29:14 ..... inserting junctions into the genome indices
Jan 25 20:29:14   Finished SA search: number of new junctions=1, old junctions=0
Jan 25 20:29:14   Finished sorting SA indicesL nInd=400

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

Could you kindly let me know what could be the reason for this error? Thanks a lot.

Best,

Yujuan

[Alexander Dobin]

Hi Yujuan,

please try to add this parameter: --limitSjdbInsertNsj 100

Cheers

Alex