search

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
403 stars 118 forks source link

RSEM: WARNING: --genomeSAindexNbases 14 is too large for the genome size=375049285, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 13 #147

Open Rohit-Satyam opened 3 years ago

Rohit-Satyam commented 3 years ago

Hi!

I was trying running RSEM on rice genome. However I end up getting this error.

nohup: ignoring input and appending output to 'nohup.out' !!!!! WARNING: --genomeSAindexNbases 14 is too large for the genome size=375049285, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 13 It says to add --genomeSAindexNbases 13 but there isn't an option when we prepare a reference indexes to mention this option.

Should I ignore this warning?

The command used is as follows:

nohup rsem-prepare-reference -p 8 --gtf /home/baadalvm/raw_data/Oryza_sativa.IRGSP-1.0.47.chr.gtf --star --star-path /home/baadalvm/miniconda3/envs/rice/bin /home/baadalvm/raw_data/Oryza_sativa.IRGSP-1.0.dna.toplevel.fa /home/baadalvm/raw_data/index/oryza 2> rsem.stderr &

enviroalexx commented 3 years ago

Hello, I am running into the same issue. How can we alter/add the --genomeSAindexNbases command to the RSEM prepare reference with STAR pipeline? I also need to change it from the default of 14 to 13 because of the size of the fish genome I am working with. Thank you!! -Alex

Rohit-Satyam commented 3 years ago

Sorry! Couldn't figure it out in RSEM so I switched to STAR aligner