Bowtie2 align error

Question

[sambioinfo2018]

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

[lakhujanivijay]

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

[sambioinfo2018]

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

[lakhujanivijay]

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

[sambioinfo2018]

i have given the proper index file

[Bastien Hervé]

Memory issues ? How many RAM do you have ?

[sambioinfo2018]

The memory available is 128 GB.

[GenoMax]

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

[sambioinfo2018]

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

[GenoMax]

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

[Mehmet]

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

[Bastien Hervé]

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 ?

[sambioinfo2018]

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