Entering edit mode
4.3 years ago
Chvatil
▴
130
Hello I need to map reads on a genome in fasta file format.
For that I installed Bowtie2 v2.4.1
(last version) with biodonda by doing :
conda install bowtie2
Everything went right and I can run bowtie2 properly.
But I need to use the --sra-acc
option and in the documentation they say :
As of version 2.3.5 bowtie2 now supports aligning SRA reads. Prepackaged builds will include a package that supports SRA
and unfortunatly when I use this option I get :
/beegfs/data/my_conda/bin/bowtie2-align-s: unrecognized option '--sra-acc'
So I wondered if you got the same issue when installing bowtie2 with bioconda and if you have a solution in order to add this particular option ?
Thank you for your help.
Please provide full command line you are using.
I built my db with :
then I ran :
I think your copy of
bowtie2
has not been compiled withsra
support, if you or someone compiled it locally.Download the pre-compiled binary if you can.
I tried to dowload
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.1/bowtie2-2.4.1-linux-x86_64.zip
but I still get the same issue it does not recognise the '--sra-acc' option...Can you try with just one SRA accession?
It is the same, this is the option that is not recognized