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alexdobin / STAR

RNA-seq aligner
MIT License
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STAR requesting significantly more RAM than genome size #1256

Open kushagrasharma opened 3 years ago

kushagrasharma commented 3 years ago

Hi!

I'm trying to use STAR to index an axolotl genome (~900MB). When I run the following command - STAR --runThreadN 1 --runMode genomeGenerate --genomeDir /Users/kushagrasharma/coding/chenlab/star_indexes/axolotl/index --genomeFastaFiles /Users/kushagrasharma/coding/chenlab/star_indexes/axolotl/genome_files/Axolotl.Trinity.CellReports2017.fasta --sjdbGTFfile /Users/kushagrasharma/coding/chenlab/star_indexes/axolotl/genome_files/fixed_axoltl.gtf, I get the following error. 

Jun 01 17:03:04 ..... started STAR run
Jun 01 17:03:04 ... starting to generate Genome files

EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM=31000000000is too small for your genome
SOLUTION: please specify --limitGenomeGenerateRAM not less than 1086363184053 and make that much RAM available

Jun 01 17:03:12 ...... FATAL ERROR, exiting

This is more RAM than my machine has, and it seems off since my machine is able to work with genomes larger than the axolotl's with STAR. Is there some error happening here?

alexdobin commented 3 years ago

Hi Kushagra,

what's the total size of the fasta file, and how many "chromosomes" are in it? Since it looks like a de-nov assembly by Trinity, it probably contains a large number of transcripts. In this case, you would need to scale --outSAMattrRGline as log2(GenomeLength/NumberOfReferences) (but no more than 18 which is default).

Cheers Alex