STAR aligner - Segmentation fault (core dumped) multiple fastq paired-end samples

deepbiomed

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Join Date: Apr 2013

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STAR aligner - Segmentation fault (core dumped) multiple fastq paired-end samples

10-29-2016, 10:00 PM

Hi,
I am using STAR-2.5.2b on virtualbox with 65 gb of RAM assigned and 28 CPUs/threads.
When I ran STAR with single paired-end sample, it worked like a charm, very quick compared to TopHat but when I am trying to run STAR with multiple samples, I got the core dumped error.

1) VirtualBox:/media/sf_John/star/CR004/test_together_,$ '/media/sf_John/star/STAR-2.5.2b/bin/Linux_x86_64/STAR' --runThreadN 28 --sjdbOverhang 99 --genomeDir '/media/sf_John/star/genome_build' --readFilesIn '/media/sf_John/star/CR004/samples/CR004_S24_L005_R1_001.fastq', '/media/sf_John/star/CR004/samples/CR004_S24_L005_R2_001.fastq' '/media/sf_John/star/CR004/samples/CR004_S24_L006_R1_001.fastq', '/media/sf_John/star/CR004/samples/CR004_S24_L006_R2_001.fastq' --outFileNamePrefix SampleA --chimSegmentMin 20

Segmentation fault (core dumped)

also tried

2) VirtualBox:/media/sf_John/star/CR004/test_together_,$ '/media/sf_John/star/STAR-2.5.2b/bin/Linux_x86_64/STAR' --sjdbOverhang 99 --genomeDir '/media/sf_John/star/genome_build' --readFilesIn /media/sf_John/star/CR004/samples/*.fastq --outFileNamePrefix SampleA --chimSegmentMin 20

Segmentation fault (core dumped)

same error. I know this has to do something with memory but don't know how to resolve it.

Please guide.
Thanks
D
Tags: core dumped, multiple fastq, rna-seq, star
wdecoster

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Join Date: Oct 2015

Posts: 97
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10-30-2016, 12:10 PM

Cross posted
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STAR aligner - Segmentation fault (core dumped) multiple fastq paired-end samples

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