Cannot insert sequence on the fly because of strand GstrandBit problem

[Lynne Hagelthorn]

I'm using STAR for the first time. My lab member gave me a previously used reference genome and gtf. When I try to run it reads 

Jan 13 19:43:57 ..... started STAR run

Jan 13 19:43:57 ..... loading genome

And then gives the error 

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

I've attached the log.out file and I'm not sure what's causing this issue. The error occurs when it states

Jan 13 19:45:07 ..... inserting extra sequences into genome indexes

Thank you for any help you can provide.

[Alexander Dobin]

Hi @lynnehagelthorn

please remove these options from the command line - they are only used at the genome generation step, not at the mapping step:

--genomeFastaFiles /global/scratch/lynnehagelthorn/trim/Trimmomatic-0.39/HanXRQr2.0-SUNRISE-2.1_nebraska_consensus.fa --sjdbGTFfile /global/scratch/lynnehagelthorn/trim/Trimmomatic-0.39/HanXRQr2.0-SUNRISE-2.1_nebraska_consensus.gtf 

Also, since your fast files are gzipped, you would need to add

--reafFilesCommand zcat

Cheers

Alex