alexdobin / STAR

RNA-seq aligner

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Long time genome indexing

esraagithub opened this issue · comments

commented

hello
i run star aligner indexing command. it takes 7 days and still working right now.
my server is 48 ram

the reference genome is a combined reference. genome of human Hg38 and other microorganisms
here is the tail of the log file:

Number of chunks: 129; chunks size limit: 979802960 bytes
Apr 15 17:03:58 ... sorting Suffix Array chunks and saving them to disk...

here is files created in the output folder:
-rw-r--r-- 1 root root 10240 Apr 15 17:02 chrLength.txt
-rw-r--r-- 1 root root 28683 Apr 15 17:02 chrNameLength.txt
-rw-r--r-- 1 root root 18443 Apr 15 17:02 chrName.txt
-rw-r--r-- 1 root root 16377 Apr 15 17:02 chrStart.txt
-rw-r--r-- 1 root root 27217328 Apr 15 17:02 exonGeTrInfo.tab
-rw-r--r-- 1 root root 14634844 Apr 15 17:02 exonInfo.tab
-rw-r--r-- 1 root root 46 Apr 15 17:02 geneInfo.tab
-rw-r--r-- 1 root root 384535224 Apr 15 17:03 Log.out
-rw-r--r-- 1 root root 5198482 Apr 15 17:02 sjdbList.fromGTF.out.tab
-rw-r--r-- 1 root root 4525423 Apr 15 17:02 transcriptInfo.tab

here is my code:
STAR-2.7.11b/bin/Linux_x86_64/STAR --runMode genomeGenerate
--runThreadN 11
--genomeDir star_output
--genomeFastaFiles ref.fasta
--sjdbGTFfile ref.gtf
--sjdbOverhang 90