Question: Bowtie2 error during alignment
0
gravatar for xiaoyi.wang
10 days ago by
xiaoyi.wang10
xiaoyi.wang10 wrote:

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 • 97 views
ADD COMMENTlink modified 10 days ago by genomax224k • written 10 days ago by xiaoyi.wang10

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 REPLYlink written 10 days ago by genomax224k

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 REPLYlink written 8 days ago by xiaoyi.wang10

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 REPLYlink written 9 days ago by mks00230
1

Thanks! I will try.

ADD REPLYlink written 8 days ago by xiaoyi.wang10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1527 users visited in the last hour