BowTie2 in the system path?

Microbial community profiling MetaPhlAn
1

Hi,

I’m trying to run strainphlan ultimately but first having trouble with metaphlan.
I installed metaphlan through anaconda, and the version installed is: metaphlan 3.0 (pyh5ca1d4c_2).

First command I ran:
metaphlan 6A_R1_001.fastq.gz,6A_R2_001.fastq.gz -s metagenome6A.sam.bz2 --bowtie2out metagenome6A.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_metagenome6A.txt

This created 6 bt.2 files in the metaphlan database directory. But then gave this error:
Fatal error running BowTie2. Is BowTie2 in the system path?

Bowtie is installed at: /opt/anaconda3/bin/bowtie2

I also tried this:
metaphlan 6A_R1_001.fastq.gz,6A_R2_001.fastq.gz -s metagenome6A.sam.bz2 --bowtie2db /opt/anaconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases -x mpa_v30_CHOCOPhlAn_201901 --bowtie2out metagenome6A.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_metagenome6A.txt
which failed with the same error.

What could be the problem? Thank you already for your time on this!

2

MetaPhlAn is unable to find the bowtie2 executable, can you check if /opt/anaconda3/ is present in $PATH?

Otherwise, you can specify the executable’s location with the --bowtie2_exe parameter (--bowtie2_exe /opt/anaconda3/bin/bowtie2.

3

Thank you for the quick response but I’m still having the same issue.
I tried both of your suggestions but none worked. Here’s the error:

Possible unintended interpolation of @mac in string at /opt/anaconda3/lib/5.30.3/darwin-thread-multi-2level/Config_heavy.pl line 250.
Possible unintended interpolation of @mac in string at /opt/anaconda3/lib/5.30.3/darwin-thread-multi-2level/Config_heavy.pl line 1177.
Global symbol “@mac” requires explicit package name (did you forget to declare “my @mac”?) at /opt/anaconda3/lib/5.30.3/darwin-thread-multi-2level/Config_heavy.pl line 250.
Global symbol “@mac” requires explicit package name (did you forget to declare “my @mac”?) at /opt/anaconda3/lib/5.30.3/darwin-thread-multi-2level/Config_heavy.pl line 1177.
Compilation failed in require at /opt/anaconda3/lib/5.30.3/darwin-thread-multi-2level/Config.pm line 105.
OSError: “Command ‘[‘bowtie2’, ‘-h’]’ returned non-zero exit status 255.”
Fatal error running BowTie2. Is BowTie2 in the system path?

I can run bowtie2 by just calling it, so it must be in the system path…

4

What does it print if you run bowtie2 -h? Have you installed MetaPhlAn in an environment different than the “base” one?

5

Actually, that’s the problem. I cannot run it (bowtie2 -h). If I do:

Possible unintended interpolation of @mac in string at /opt/anaconda3/lib/5.30.3/darwin-thread-multi-2level/Config_heavy.pl line 250.
Possible unintended interpolation of @mac in string at /opt/anaconda3/lib/5.30.3/darwin-thread-multi-2level/Config_heavy.pl line 1177.
Global symbol “@mac” requires explicit package name (did you forget to declare “my @mac”?) at /opt/anaconda3/lib/5.30.3/darwin-thread-multi-2level/Config_heavy.pl line 250.
Global symbol “@mac” requires explicit package name (did you forget to declare “my @mac”?) at /opt/anaconda3/lib/5.30.3/darwin-thread-multi-2level/Config_heavy.pl line 1177.
Compilation failed in require at /opt/anaconda3/lib/5.30.3/darwin-thread-multi-2level/Config.pm line 105.

I’m not very sure but i don’t think i installed metaphlan in a different environment because when i run conda list, both are there.
bowtie2 2.4.1 py37h5e6fd57_3 bioconda
metaphlan 3.0 pyh5ca1d4c_2 bioconda

And this is how I installed metaphlan:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda install -c bioconda python=3.7 metaphlan=3.0=pyh5ca1d4c_2 --no-channel-priority

6

You should try to install MetaPhlAn in a new clean environment to avoid incompatibilities. In a new environment with just Python 3.7 (conda create -n metaphlan-3.0 python=3.7), install the latest MetaPhlAn build (conda activate metaphlan-3.0 && conda install metaphlan=3.0.3). This will install all the dependencies and the latest version, the build you forced the installation is quite old and affected by several bugs.

7

Yes!! It solved the problem! Thank you so much :slight_smile: