cannot insert sequence on the fly because of strand GstrandBit problem

[zheny...@webmail.hzau.edu.cn]

STAR --runMode alignReads --runThreadN 16 --genomeDir /home/genome/ --genomeFastaFiles /home/genome/genome.fa --sjdbGTFfile /home/genome/genome.gtf --readFilesIn /RNA-Seq_cleanreads/C6_B_1.clean.fq /RNA-Seq_cleanreads/C6_B_2.clean.fq --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outBAMsortingThreadN 8 

My command line is here. I don't know what happened. But it says "EXITING because of FATAL ERROR: cannot insert sequence on the fly because of strand GstrandBit problem". How should I do?

[Alexander Dobin]

Hi @ zhenyueran

please send me Log.out of this run.

Cheers

Alex

[Alexander Dobin]

Hi @ zhenyueran

it looks like at the mapping stage you are using --genomeFastaFiles with the same file as the one used at the genome generation step.

I think this causes the problem - please try to map without this parameter.

Cheers

Alex

--genomeFastaFiles /home/yueran/RNA_seq/STAR/genome/Sus_scrofa.Sscrofa10.2.dna.toplevel.fa      

[Hani Goodarzi]

Hi,

I have a similar problem:

⇒  STAR --readFilesCommand zcat --runThreadN 12 --sjdbGTFfile /nvme/genomes/hg19/hg19_genes.gtf  --genomeDir /nvme/genomes/hg19 --genomeFastaFiles /nvme/genomes/hg19/hg19.fa --readFilesIn MDA_shControl_r1_S7.fastq.gz --outFileNamePrefix MDA_shControl_r1_S7_

Aug 11 17:50:54 ..... started STAR run

Aug 11 17:50:54 ..... loading genome

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

SOLUTION: please contact STAR author at https://groups.google.com/forum/#!forum/rna-star

Aug 11 17:58:59 ...... FATAL ERROR, exiting

- H

[Alexander Dobin]

Hi Hani, 

please send me the Log.out file of this run.

Cheers

Alex

[Hani Goodarzi]

Hi Alex, it turns out it was the same issue of using the same fasta and genomeDir. Removing the --genomeFastaFiles parameter solved the issue.