Bowtie2 error during alignment

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7.7 years ago

xiaoyi.wang ▴ 10

Hi All: I am new to RNA-seq data analysis. When I was using bowtie2 for alignment. I encountered the following error message:

bowtie2 --no-unal -x /ysm-gpfs/datasets/genomes/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/genome -U /ysm-gpfs/home/xw332/project/TCGA/trimmed/C_01.fq -S /ysm-gpfs/home/xw332/project/TCGA/aligned/C_01.sam

***(ERR): bowtie2-align died with signal 7 (BUS)***

Any idea how this happened? What does signal 7 mean? Desperate for some help here. Thanks.

RNA-Seq alignment • 3.2k views

ADD COMMENT • link updated 7.3 years ago by Biostar 20 • written 7.7 years ago by xiaoyi.wang ▴ 10

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Are you running this on a cluster? What version of bowtie2 are you using? Is this a known working installation of biowtie2? signal 7 indicates bad memory access.

ADD REPLY • link 7.7 years ago by GenoMax 147k

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yeah. On a cluster. But it's only one sample. so don't know why there isn't enough computer memory. The bowtie2 installed on the cluster is Bowtie2/2.2.9-foss-2016a, not the latest version. Could this be the reason?

ADD REPLY • link 7.7 years ago by xiaoyi.wang ▴ 10

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One thing you can do is take a subset of your total reads, say 1000 subset reads and then try to align these reads using bowtie2.

For taking subset u can use the command below

seqtk sample -s100 C_01.fq 1000 > C_01_Subset.fq

This might help you to resolve the issue and find why the error is coming.

ADD REPLY • link 7.7 years ago by mks002 ▴ 220

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Thanks! I will try.

ADD REPLY • link 7.7 years ago by xiaoyi.wang ▴ 10

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