STAR index generation killed after "inserting junctions into the genome indices"

Question

[becky.reese]

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!!

Answer 1

[dsull]

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.

[becky.reese]

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