Issue with bowtie2db trying to install MetaPhIan3

[timyerg]

Hi!
Here is another person with the same problem

Bowtie2 align error

Hi I am new to Metaphlan3, I installed using miniconda3 and build the database in folder outside conda environment and i gave the following commands to run the file. $ metaphlan 945_metagenome_1.fastq.gz, 945_metagenome_2.fastq.gz --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_metagenome.txt --bowtie2db “/home/bsadaiappan/Metaphlan_databases/” -x mpa_v30_CHOCOPhlAn_201901 And i got this error /home/bsadaiappan/miniconda3/envs/mpa/bin/bowtie2-align-s: error w…

Fixed it by replacing bowtie executive files (in that case no need to add path to exe file in metaphlan commands). See the post by the link for commands.

Bowtie prebuilded can be obtained here:

Releases · BenLangmead/bowtie2