Cannot install database on my mac Metaphlan 3

Hello when I was trying to follow the installation tutorial and I realized that I couldn’t install the database properly.

(metaphlan-3.0) Cheng.Clay.Li@ChengdeMacBook-Pro decon % metaphlan --install --index mpa_v30_CHOCOPhlAn_201901 --bowtie2db /Users/Cheng.Clay.Li/Metatools/bowtie2db

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 % 4.35 MB/sec 0 min -0 sec
Downloading file of size: 0.00 MB
0.01 MB 12800.00 % 32.80 MB/sec 0 min -0 sec

Decompressing /Users/Cheng.Clay.Li/Metatools/bowtie2db/mpa_v30_CHOCOPhlAn_201901.fna.bz2 into /Users/Cheng.Clay.Li/Metatools/bowtie2db/mpa_v30_CHOCOPhlAn_201901.fna
Traceback (most recent call last):
File “/Users/Cheng.Clay.Li/opt/anaconda3/envs/metaphlan-3.0/bin/metaphlan”, line 10, in
File “/Users/Cheng.Clay.Li/opt/anaconda3/envs/metaphlan-3.0/lib/python3.7/site-packages/metaphlan/”, line 985, in main
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/Users/Cheng.Clay.Li/opt/anaconda3/envs/metaphlan-3.0/lib/python3.7/site-packages/metaphlan/”, line 304, in check_and_install_database
download_unpack_tar(index, bowtie2_db, bowtie2_build, nproc, use_zenodo)
File “/Users/Cheng.Clay.Li/opt/anaconda3/envs/metaphlan-3.0/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 “/Users/Cheng.Clay.Li/opt/anaconda3/envs/metaphlan-3.0/lib/python3.7/”, line 411, in check_output
File “/Users/Cheng.Clay.Li/opt/anaconda3/envs/metaphlan-3.0/lib/python3.7/”, line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘bowtie2-build’, ‘–usage’]’ returned non-zero exit status 250.

appear to be similar with the problem in an older thread.

I reinstalled my mpa according to

but the problem still exists. :confused:

Many thanks.


Problem fixed.

I reinstalled the metaphlan couple of times based on issue 109 and the installation seems working properly now.