STAR 2.3.0e Linux dna 3.2.0-41-generic #66-Ubuntu SM

THIS WORKED: * The fasta file is a 2.8 Mbp bacteria

STAR --runMode genomeGenerate --genomeDir ref --genomeFastaFiles 6008.fna --runThreadN 32

THIS CORE DUMPED: * Read file is FASTQ, 31bp reads, in Phred+64 format.

Core was generated by `STAR --genomeDir ref --readFilesIn 6008_mRNA.fastq --runThreadN 32'. Program terminated with signal 11, Segmentation fault.

0 0x0000000000405e4b in compareSeqToGenome(char**, unsigned long long, unsigned long long, unsigned long long, char*, PackedArray&, unsigned long long, bool, bool&, Parameters*) ()

I went to the forums and dug around.

It seems to work if I add "--genomeSAindexNbases 2" to the index generation step, as suggested by another user for small genomes.

I still consider a core dump a bug however :-)

Could you stat() the genome files to estimate the genome sizes and auto-choose good parameters to avoid this problem?

Hi Torsten,

this is indeed a bug and hope to have a fix ready for the next release in ~July.

Thanks, Alex