Question: STAR is taking a LONG time to generate mouse genome
0
gravatar for Riva
3.1 years ago by
Riva0
Riva0 wrote:

I am trying to generate the mouse genome to use for mapping my RNAseq data, however it has been running for over 4 days and still appears to be running. This seems to be too long, so I'm not sure if I have made a mistake or if I should stop the program, or what next.

I am using the Linux command line and have 100 GB free and am allocating 4 cores to run STAR. I used the following command and have gotten as far as it shows below. Now the command line just has a blinking white cursor.

STAR --runMode genomeGenerate --genomeDir /home/riva/Desktop/RNAseqPLN/genomeDir --genomeFastaFiles /home/riva/Desktop/RNAseqPLN/GRCm38.p4.genome.fa --sjdbGTFfile /home/riva/Desktop/RNAseqPLN/gencode.vM10.chr_patch_hapl_scaff.annotation.gtf --sjdbOverhang 100 --runThreadN 4

Oct 06 10:00:10 ..... Started STAR run

Oct 06 10:00:10 ... Starting to generate Genome files

Oct 06 10:00:56 ... starting to sort Suffix Array. This may take a long time...

Oct 06 10:01:09 ... sorting Suffix Array chunks and saving them to disk...

rna-seq • 2.6k views
ADD COMMENTlink written 3.1 years ago by Riva0
1

It looks like you are doing this on a personal computer. How much RAM do you have? STAR requires 30GB for a human genome, so mouse should be similar.

Check this previous discussion: STAR aligner generating genomes takes long time

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by igor8.8k

Did you check if a similar problem was already described in STAR Google Group? I always found solution to aaaall my STAR problems there.

Cheers.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Marge280

Try increasing the threads --runThreadN 8.

ADD REPLYlink written 3.1 years ago by Ron980

Thank you all for your feedback. I did try to work out what my problem was with the previous discussion listed by Igor before I posted, however I thought I was having a different issue. I am quite embarrassed about my mistake, but I will list it here just in case there is some other person out there who does the same thing. So, I confused RAM with Hard drive space (I know, I'm sorry!, please don't yell at me in your heads as you look at the computer screen and read this, instead let this be your comical relief for the day and just laugh) and I thought I had plenty of "RAM" when really I just had a bunch of hard drive space. It is very clear now that my problem is not having enough RAM, as you and others have suggested in other posts. I ended up doing a quick run with HISAT2 to just get an idea of what my data looked like. I do appreciate your suggestions and I will likely use those as well when I get access to a server that can handle STAR.

ADD REPLYlink written 3.0 years ago by Riva0
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