search

alexdobin / STAR

RNA-seq aligner
MIT License
1.77k stars 497 forks source link

EXITING because of FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem #2105

Open sukhmanpreet33 opened 3 months ago

sukhmanpreet33 commented 3 months ago

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

alexdobin commented 2 months ago

Hi @sukhmanpreet33

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