RNAseq, indexing with STAR

Question

[MOJ]

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

[h.mon]

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?

[MOJ]

human.refseq.gff.gtf is 227M Genomic.fna is 3.1GB

[Matina]

Can you maybe post the command you are using?

[MOJ]

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

[Matina]

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.

[shuksi1984]

Thanks Matina for the link. I worked for me..:)