"Killed: 9" message when trying to run STAR

[Krithika B]

Hello,

I am trying out STAR alignment for the first time (on my mac). I am using the hg19 pre compiled reference provided here: http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/UCSC/hg19_noAnnotations/

This is the command I used:

cd /star/STAR-master/bin/MacOSX_x86_64

./STAR --runThreadN 4 \

--genomeDir /Users/ls483/Documents/STAR_ref \

--readFilesIn /Users/ls483/Documents/GEO/input/sample_1.fastq.gz /Users/ls483/Documents/GEO/input/sample_2.fastq.gz \

--readFilesCommand gunzip -c \

--outReadsUnmapped Fastx \

--sjdbGTFfile /Users/ls483/Documents/STAR_ref/2013Oct10_hg19GTF_UCSC.gtf \

--outSAMtype BAM SortedByCoordinate \

--outFileNamePrefix /Users/ls483/Documents/GEO/output/star1

But it gave a "Killed: 9" message

Link to Log.out file on google drive  https://drive.google.com/file/d/0B3-883ME4sP3R1VnVW9LaE1rdlk/view?usp=sharing

Could someone please tell me what is the problem ? 

Thanks,

K

[Alexander Dobin]

Hi Krithika

how much RAM do you have? This error is sometimes caused by RAM overflows.

If you have <32GB, try to use --limitSjdbInsertNsj 300000 to reduce RAM consumption.

Cheers

Alex

[Krithika B]

Thanks for the feedback, I will try your command , Mine is a 16GB Mac book pro

[Alexander Dobin]

16GB is not enough for human genome with default parameters, you need >30GB.

To fit it into 16GB you would need to re-generate the genome with:

STAR --runMode genomeGenerate --genomeDir ./ --runThreadN 4 --genomeFastaFiles genome.fa --sjdbGTFfile annot.gtf --genomeSAsparseD 2 --limitSjdbInsertNsj 300000 --limitGenomeGenerateRAM 14000000000

[Krithika B]

Tried the command like you said, still get the same "killed: 9" error. Any other suggestions ? 

[Alexander Dobin]

Hi Krithika, 

please send me the Log.out file of this run.

Cheers

Alex