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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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Star Index Out of Ram Issue #135

Open mbcouger opened 4 years ago

mbcouger commented 4 years ago

Hello Deweylab,

I am running into the following issue when preparing reference with STAR is there an option to add for this or a place you can suggest I change in the scripting/code

EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM=31000000000is too small for your genome SOLUTION: please specify --limitGenomeGenerateRAM not less than 168632718037 and make that much RAM available

Many Thanks, Brian

anupambh commented 4 years ago

Hi, I am facing the same issue while generating Human Genome.(GRCh38).

command: /opt/rsem/RSEM-1.3.3/rsem-prepare-reference --gtf GRCh38.gtf --star --star-path /home/bif/app/STAR-master/bin/Linux_x86_64/ -p 40 GRCH38.fa /storage1/bif_work/rsem_reference/GRCh38

While I am using parsing -- limitGenomeGenerateRAM=156410676608 in the above command, it says "unknown command".

Any help would be appreciated.

Thanks in advance.

Regards; Anupam

pgupta3005 commented 2 years ago

Hi, I am facing the same issue. Were you able to solve the problem?

pgupta3005 commented 2 years ago

For record, it is suggested to build STAR indices out of RSEM and use that for mapping. Then the *Aligned.toTranscriptome.out.bam output from STAR and be used for rsem-calculate-expression https://groups.google.com/g/rsem-users/c/CsS4KCYKseg