This is a test version of Biostars. For the public version, visit https://www.biostars.org.
STAR index generation killed after "inserting junctions into the genome indices"

I am having trouble generating an index with STAR. It always kills at "inserting junctions into the genome indices". I have 32GB of RAM and I tried limiting the RAM used, but that didn't seem to work. Are there other flags I can try before I resort to buying another stick of RAM?

STAR --runThreadN 12 --runMode genomeGenerate -genomeDir ./ --genomeFastaFiles Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile Homo_sapiens.GRCh38.110.gtf --sjdbOverhang 149 --limitGenomeGenerateRAM 28000000000

I can figure out how to upload the log file if that is helpful

Thanks!!

star index rna-seq killed
• 1,764 views • link
written by becky.reese • becky.reese

1 answer

Try the --genomeSAsparseD option (set it to 2 or maybe 3).

Also, you can use put /usr/bin/time -v at the beginning of the command to get your RAM usage for running that command.

• 0 views • link
updated by ATpoint ATpoint • written by dsull dsull

This worked!! Thank you so much!! And thank you for the tip on the RAM usage command as well

• 0 views • link
written by becky.reese • becky.reese

Log in to answer this question.

More posts like this