STAR alignment killed: 9

[Olivia Estevez]

Dear Dr. Dobin,

I am trying to use STAR to align human RNAseq reads in fastq format using the human genome as a reference. 

I have generated the genome indexes on the Human Genome Hg38 from ensemble and obtained the following files (saved at the same direcrtory as the HumanGenome.fasta file):

612  5 oct 12:04 genomeParameters.txt

4088  5 oct 12:04 chrLength.txt

8109  5 oct 12:03 chrName.txt

5845  5 oct 12:01 chrStart.txt

43499651072  5 oct 12:00 Genome

28276333298  5 oct 10:45 SA

1744830588  5 oct 09:59 SAindex

58538  5 oct 09:55 Log.out

44151031456  2 oct 12:51 Homo_sapiens.GRCh38.dna.toplevel.fa

Now i am trying to make the alignment using the following script:

#!/bin/bash -ve                                                                 

#module load jdk-sun/1.7.0                                                      

### Genome reference:                                                          

#  http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/ENSEMBL/homo_sapiens/ENSEMBL.homo_sapiens.release-75/  

                         

bindir=/Users/emitb643558/STAR/bin/MacOSX_x86_64

genomeDir=/Users/emitb643558/Hg38_STAR

#fastq:                                                                  

fastqDir=/Users/emitb643558/desktop/RNAseq_Olivia/OLI.fastq

#alignment STAR:                                                                

$bindir/STAR --genomeDir $genomeDir --readFilesIn $fastqDir --runThreadN 32 -verbose

And I get the this error:

$bindir/STAR --genomeDir $genomeDir --readFilesIn $fastqDir --runThreadN 32 -verbose

Oct 06 10:40:23 ..... Started STAR run

Oct 06 10:40:23 ..... Loading genome

./STAR1pass.sh: line 17:   600 Killed: 9               $bindir/STAR --genomeDir $genomeDir --readFilesIn $fastqDir --runThreadN 32 -verbose

I am using an iMac with 32G Ram. Is this enough? Is the error due to memory issues? 

I am new at this and I cannot find out what I am doing wrong here and why this is not working. if you could help me out it would be of great help.

Thanks in advance,

Olivia

[Alexander Dobin]

Hi Olivia,

are you trying to map with the genome indexes you generated, or with the one you downloaded?

Please send me the Log.out file of the failed run.

Cheers

Alex