I am wrking on RNAseq. I am using STAR for indexing. It generates all the files except the genome file.I am running the command on 30G RAM and 400G hard disk and 2 runthread. It took 2 days and is still running. Any opinion will be appreciated
What is the assembly quality / level? Hundreds of thousands contigs, hundreds or a few thousands scaffolds, or tens of chromosomes? What is the size in gigabytes of the genome file?
human.refseq.gff.gtf is 227M
Genomic.fna is 3.1GB
Can you maybe post the command you are using?
When I used following command, several SA index files are generated.
/path/to/star/STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /path/to/star/genome_file --genomeFastaFiles /path/to/star/GCF_000001405.31_GRCh38.p5_genomic.fna --sjdbGTFfile /path/to/star/human.refseq.gff.gtf --sjdbOverhang 100 --limitGenomeGenerateRAM=8825541333
I cant see anything wrong with this command. This is weird indeed. Why don't you try and post your question here at the official rna-star forum. The developer of STAR (Alex Dobin) is great - always replies to posts and he is super helpful.
Thanks Matina for the link. I worked for me..:)
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