Bowtie2 align error
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
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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
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
the index base is
25refthen the command should bei have given the proper index file
Memory issues ? How many RAM do you have ?
The memory available is 128 GB.
Did you compile this program yourself or download a precompiled binary?
No. It was already installed on the server i am using
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_towith a real value on your computer).std::bad_alloc'is a memory problem, meaning the memory that you used is not sufficient.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 ?
Hi All, Thanks for your comments. The size of index file is 35 GB
Hi All, Thanks for your comments. The size of index file is 35 GB