am currently using MetaPhlAn version 3.0.13 which I downloaded through conda install. As instructed in the manual, I downloaded the database in a folder outside the Conda environment, by running this:
$ metaphlan --install --bowtie2db
Then I tried the following code with two fastq.gz forward and reverse reads for one sample and indicated the database location as follows:
$ metaphlan P001-READ1-Sequences.txt.gz,P001-READ2-Sequences.txt.gz --bowtie2db /data/homezvol2/cirodri1/bowtie2db_folder --bowtie2out metagenome.bowtie2.bz2 --input_type fastq -o profiled_metagenome.txt
But when running that code I get the following error:
I have been checking through the github issues channel and found a similar issue #157 but the issue was closed by the user without a solution.
Then, I tried running the following code on the same set of fastq.gz files:
$ for f in .gz*
do
echo “Running metaphlan 3.0 on ${f}”
bn=$(basename ${f%fastq.bz2})
metaphlan $f --input_type fastq -s sams/${bn}.sam.bz2 --bowtie2db /data/homezvol2/cirodri1/bowtie2db_folder --bowtie2out bowtie2/${bn}.bowtie2.bz2 -o profiles/${bn}_profile.tsv
done
and I obtained the following error:
Can anyone guide me into making my Metaphlan work correctly and locate the database. Thank you!
- Version: 3.0.13
- Download source through conda create --name mpa -c bioconda python=3.7 metaphlan
- I am running the program from a remote server and inside a miniconda self-made environment.
