'Segmentation fault (core dumped) STAR alignment

Im really new to the RNA seq field and are trying to align my data to a viral genome with STAR. However , I constantly get the error noted below. I've tried to change the amount of nodes (10), number of threads (48) and have around 200G of memory to run my job, but this does not seem to help... Any advice?

code: Dec 24 19:09:40 ..... started STAR run

Dec 24 19:09:40 ..... loading genome

Dec 24 19:09:41 ..... started mapping Segmentation fault (core dumped)'

Thanks!

Solution 1:^[1]

How did you create the STAR index? I'm asking because it depends on the genome's size (I guess yours is very small since it's viral) and maybe you are using the default and not optimal value.

According manual's instructions:

For small genomes, the parameter --genomeSAindexNbases must to be scaled down, with a typical value of min(14, log2(GenomeLength)/2 - 1). For example, for 1 megaBase genome, this is equal to 9, for 100 kiloBase genome, this is equal to 7.

STAR --runThreadN 16 \
     --runMode genomeGenerate \
     --genomeDir </path/to/your/starIndex/directory> \
     --genomeFastaFiles </your/reference/file> \
     --genomeSAindexNbases <your_numerical_value>

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Solution 1	jgarces

'Segmentation fault (core dumped) STAR alignment

Solution 1:[1]

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Solution 1:^[1]