Question: STAR aligner - Segmentation fault (core dumped) multiple fastq paired-end samples
0
gravatar for deep.pandya
2.6 years ago by
deep.pandya0 wrote:

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) d9@d9-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) d9@d9-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

ADD COMMENTlink modified 2.6 years ago by genomax67k • written 2.6 years ago by deep.pandya0
2

I don't think STAR can take multiple paired-end samples as a single command. Try STAR ... --readFilesIn read1.fq read2.fq, then repeat and rinse for other samples you may have.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Eric Lim1.4k

So you meant, I have to run each sample individually ?

ADD REPLYlink written 2.6 years ago by deep.pandya0

Yes indeed. Why would you want to run samples together?

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k

I wanted to run samples in a batch instead of together in a same code.

ADD REPLYlink written 2.6 years ago by deep.pandya0
1

You can run them sequential using a bash loop or using gnu parallel.

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k

Thank you, i will work on it .

ADD REPLYlink written 2.6 years ago by deep.pandya0

Hello deep.pandya!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=200491#post200491

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k

Sorry, I did not know I can post it in only one forum. I will delete Seqanswers one

ADD REPLYlink written 2.6 years ago by deep.pandya0

There is no rule that mandates posting to just one site but many people who answer questions participate on both sites and as such posting on just one site prevents duplication of effort for people who are helping others.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax67k
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