Hi everyone, I´m a masters student and new at bioinformatics. My research is in RNA-Seq analysis, and right now I´m having trouble to generate the genome indexes prior to the alignment in STAR. A couple minutes after lauching the command line, an error message apears that the analysis was aborted by the user, a while after the message "sorting Suffix Array chunks and saving them to disk". I´m trying to execute the command on a linux environment, through WinSCP. Apparently the parameters are correct, including the number of threads used. I don´t know where the problem might be. Any guesses?
This is the command:
/opt/STAR-2.7.9a/bin/Linux_x86_64/STAR --runThreadN 20 --runMode genomeGenerate --genomeDir /home/julia.nicoliello/genome_index --genomeFastaFiles /home/julia.nicoliello/genoma-fasta/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /home/julia.nicoliello/GRCh38.101/Homo_sapiens.GRCh38.101.chr.gtf
And these are the links to the files I´ve dowmloaded:
http://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/ http://ftp.ensembl.org/pub/release-101/gtf/homo_sapiens/
Thank you so much!
How much memory do you have available? Generating STAR indexes requires at least 30-40G of free RAM (if not more).
Hi! The problem actually was in the number of threads, after setting the runThreadsN parameter to 16 it was possible to complete de command. Thank you!