Question: Bowtie2 align error
0
gravatar for sambioinfo2018
10 months ago by
sambioinfo20180 wrote:

Hi All,

While performing alignment using Bowtie2, i get the following error: Error: Encountered exception: 'std::bad_alloc' (ERR): bowtie2-align exited with value 1

My alignment command is as follow: bowtie2 -x Refgenome -1 Read_R1_001.fastq.gz -2 Read_R2_001.fastq.gz -S alignedfile.sam

Could anyone help me in understanding the error.

Thanks in advance

alignment • 356 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 10 months ago by sambioinfo20180

Such basic questions could be easily googled. Anyways, you must check your bowtie2 index prefix. Adding your indexing command here will help others to look into the issue

ADD REPLYlink written 10 months ago by bioExplorer3.7k

I actually googled but could not find any answer. so wrote here Here is the index command: bowtie2-build -p 20 -f SeqRef.fasta 25Ref

ADD REPLYlink written 10 months ago by sambioinfo20180

the index base is 25ref then the command should be

 bowtie2 -x 25ref -1 Read_R1_001.fastq.gz -2 Read_R2_001.fastq.gz -S alignedfile.sam
ADD REPLYlink written 10 months ago by bioExplorer3.7k

i have given the proper index file

ADD REPLYlink written 10 months ago by sambioinfo20180

Memory issues ? How many RAM do you have ?

ADD REPLYlink written 10 months ago by Bastien Hervé3.7k

The memory available is 128 GB.

ADD REPLYlink written 10 months ago by sambioinfo20180

Did you compile this program yourself or download a precompiled binary?

ADD REPLYlink written 10 months ago by genomax63k

No. It was already installed on the server i am using

ADD REPLYlink written 10 months ago by sambioinfo20180

Have you tried @Vijay's suggestion above. I will suggest the following modification if your index files are in a different directory than your data files (replace path_to with a real value on your computer).

bowtie2 -x /path_to/25ref -1 Read_R1_001.fastq.gz -2 Read_R2_001.fastq.gz -S alignedfile.sam
ADD REPLYlink written 10 months ago by genomax63k

std::bad_alloc' is a memory problem, meaning the memory that you used is not sufficient.

ADD REPLYlink modified 10 months ago • written 10 months ago by Mehmet460

If OP really have 128GB of RAM, he can align every genome he wants with bowtie2.

It's a memory problem but I don't think the solution is to increase memory.

How large is your index file OP ?

ADD REPLYlink written 10 months ago by Bastien Hervé3.7k

Hi All, Thanks for your comments. The size of index file is 35 GB

ADD REPLYlink written 10 months ago by sambioinfo20180
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