Installing MetaPhlAn database fails

Dear help

I have just used MetaPhlAn successfully (many times) but started a rerun because I updated MetaPhlAn. After updating MetaPhlAn didn’t work out and I removed MetaPhlAn and reinstalled it. However, when installing MetaPhlAn database, I got an error and the installation of the database failed.

I used Conda for installing MetaPhlAn.

This is the installing and the error message:

(/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan) [sinkko@puhti-login1 bioconda2_env]$ metaphlan --install

Downloading file of size: 0.00 MB
0.01 MB 31507.69 % 75.16 MB/sec 0 min -0 sec
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes

Downloading file of size: 366.62 MB
366.62 MB 100.00 % 38.44 MB/sec 0 min -0 sec
Downloading file of size: 0.00 MB
0.01 MB 12800.00 % 84.02 MB/sec 0 min -0 sec

Decompressing /scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.fna.bz2 into /scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.fna
Traceback (most recent call last):
File “/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan/bin/metaphlan”, line 10, in
File “/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan/lib/python3.7/site-packages/metaphlan/”, line 925, in main
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan/lib/python3.7/site-packages/metaphlan/”, line 301, in check_and_install_database
download_unpack_tar(index, bowtie2_db, bowtie2_build, nproc, use_zenodo)
File “/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan/lib/python3.7/site-packages/metaphlan/”, line 180, in download_unpack_tar
bt2_build_output = subp.check_output([bowtie2_build, ‘–usage’], stderr=subp.STDOUT)
File “/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan/lib/python3.7/”, line 411, in check_output
File “/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan/lib/python3.7/”, line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘bowtie2-build’, ‘–usage’]’ returned non-zero exit status 127.
(/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan) [sinkko@puhti-login1 bioconda2_env]$

Here is how database looks like after erroneous installation:
ls -lsh metaphlan/lib/python3.7/site-packages/metaphlan/metaphlan_databases

4.0K -rw-rw----. 1 sinkko project_2001318 26 Apr 9 15:48 mpa_latest
1.4G -rw-rw----. 1 sinkko project_2001318 1.4G Apr 9 15:49 mpa_v30_CHOCOPhlAn_201901.fna
342M -rw-rw-r–. 1 sinkko project_2001318 342M Jun 30 2020 mpa_v30_CHOCOPhlAn_201901.fna.bz2
4.0K -rw-rw----. 1 sinkko project_2001318 64 Apr 9 15:48 mpa_v30_CHOCOPhlAn_201901.md5
25M -rw-rw-r–. 1 sinkko project_2001318 25M Jan 20 16:57 mpa_v30_CHOCOPhlAn_201901.pkl
367M -rw-rw----. 1 sinkko project_2001318 367M Apr 9 15:48 mpa_v30_CHOCOPhlAn_201901.tar

Best, Hanna

Could you check with bowtie2 --version and bowtie2-build if the bowtie2 installation works correctly?
You can try manually build the database in the metaphlan_databases by running bowtie2-build mpa_v30_CHOCOPhlAn_201901.fna mpa_v30_CHOCOPhlAn_201901