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

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.

RNA-Seq multiple fastq STAR segmentation fault • 4.8k views
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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.

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

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

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

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

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Thank you, i will work on it .

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Hello deep.pandya!

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

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

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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.