I wrote a shell script to run STAR aligner yesterday. To build the indices, I ran the following:
~/star/code/STAR-STAR_2.4.0k/bin/Linux_x86_64/STAR --runThreadN 24 --runMode genomeGenerate --genomeDir index \ --genomeFastaFiles rn6.fa
And it built well enough for me to abort and incorporate the following commands so I can include the gtf file (without annotation, the index seems low powered)…
--sjdbGTFfile Rattus_norvegicus.Rnor_6.0.87.gtf --sjdbOverhang 99
At this point – it gets thrown out when it tries to process the gtf:
terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_check ./index.sh: line 18: 19323 Aborted (core dumped) ~/star/code/STAR-STAR_2.4.0k/bin/Linux_x86_64/STAR --runThreadN 24 --runMode genomeGenerate --genomeDir index --genomeFastaFiles rn6.fa --sjdbGTFfile Rattus_norvegicus.Rnor_6.0.87.gtf --sjdbOverhang 99
I am assuming that either there is a command I’m missing, or the gtf file is not the right one…
Any advice would be appreciated!
Hello Jeff, where did you download the genome fasta and gtf from?
From the file names you present the genome seems to be from UCSC and the gtf from ENSEMBL. If this is the case, and if these use different genome builds and/or sequences names (I do not know for rat on top of my head), that would explain the out of range error.
Looks like this was the case – the chromosome names didn’t match up (“chr1” vs. “1”)