STAR alignment speed?
1
0
Entering edit mode
5 weeks ago
a_bis ▴ 20

Hello, I'm currently running some RNA-seq experiment alignments on a server with STAR. After about two hours, looking at the head of the Log.progress.out file, I am getting a result like this:

enter image description here

My total read count for the sample is ~80,000,000 reads. Does this mean that judging by the progress in the 'Read number' column my alignment is going to take over a week? It feels like this is abnormally long. When I submitted the bash script to the queue, the script started as follows:

#!/bin/bash
#SBATCH --job-name=star
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --time=0-64:00:00
#SBATCH --output=outfile.%j
#SBATCH --error=errfile.%j

module load STAR/2.7.4

STAR --genomeDir mm39starindex/mm39starindex/index --readFilesIn WTCHG_894903_72185194_1.fastq.gz WTCHG_894903_72185194_2.fastq.gz --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFileNamePrefix alignments/WTCHG_894903_72185194

Should I have specified a longer time or more CPUs? Any advice will be really appreciated! Many thanks.

star alignment rna-seq • 336 views
ADD COMMENT
1
Entering edit mode

Less than 10% unique mapped is very low. You may want to look into that as well.

ADD REPLY
0
Entering edit mode

Thank you for the advice. I'm very new to RNA-seq read alignment -- in your experience is there a particular thing I could do to improve alignment rates? Thank you!

ADD REPLY
0
Entering edit mode

Looks like you already posted a follow-up question: Low mapping frequency on STAR

ADD REPLY
0
Entering edit mode

Hi, yes, my question subsequently changed so I thought it would be best to rephrase it. Thanks again for your advice!

ADD REPLY
1
Entering edit mode
5 weeks ago

You need to specify the number of threads STAR uses with --runThreadN 16.

ADD COMMENT
0
Entering edit mode

Thanks, that's super helpful!

ADD REPLY

Login before adding your answer.

Traffic: 1493 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6