Couldn't run the new Humann: Error message returned from metaphlan :

Hello, I have been running a bit problem with running humann on my mac.

(biobakery3) % metaphlan --version
MetaPhlAn version 3.0.14 (19 Jan 2022)
(biobakery3) % bowtie2 --version
dyld[36435]: Library not loaded: @rpath/libtbb.dylib
Referenced from: /Users/Cheng.Clay.Li/opt/anaconda3/envs/biobakery3/bin/bowtie2-align-s
Reason: tried: ‘/Users/Cheng.Clay.Li/opt/anaconda3/envs/biobakery3/bin/…/lib/libtbb.dylib’ (no such file), ‘/Users/Cheng.Clay.Li/opt/anaconda3/envs/biobakery3/bin/…/lib/libtbb.dylib’ (no such file), ‘/usr/local/lib/libtbb.dylib’ (no such file), ‘/usr/lib/libtbb.dylib’ (no such file)
(ERR): Description of arguments failed!
Exiting now …

(biobakery3) % humann --input Sample-43_R_cat.fastq
–output …/pathways/Sample-43
–remove-temp-output
–threads 4
–metaphlan /Users/****/opt/anaconda3/envs/biobakery3/bin/
–nucleotide-database /Volumes/CL\ SSD/database/chocophlan
–protein-database /Volumes/CL\ SSD/database/uniref
Output files will be written to: /Volumes/CL SSD/pathways/Sample-43
WARNING: Can not call software version for bowtie2

Running metaphlan …

CRITICAL ERROR: Error executing: /Users/****/opt/anaconda3/envs/biobakery3/bin/metaphlan /Volumes/CL SSD/merged/Sample-43_R_cat.fastq -t rel_ab -o /Volumes/CL SSD/pathways/Sample-43/Sample-43_R_cat_humann_temp_vkwzm7zr/Sample-43_R_cat_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /Volumes/CL SSD/pathways/Sample-43/Sample-43_R_cat_humann_temp_vkwzm7zr/Sample-43_R_cat_metaphlan_bowtie2.txt --nproc 4

Error message returned from metaphlan :

Downloading MetaPhlAn database
Please note due to the size this might take a few minutes

File /Users/****opt/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.tar already present!

File /Users/ /opt/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.md5 already present!
Traceback (most recent call last):
File “/Users/
/opt/anaconda3/envs/biobakery3/bin/metaphlan”, line 10, in
sys.exit(main())
File “/Users/ opt/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 985, in main
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/Users/
/opt/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/ init .py”, line 304, in check_and_install_database
download_unpack_tar(index, bowtie2_db, bowtie2_build, nproc, use_zenodo)
File “/Users/ /opt/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/ init .py”, line 180, in download_unpack_tar
bt2_build_output = subp.check_output([bowtie2_build, ‘–usage’], stderr=subp.STDOUT)
File “/Users/
/opt/anaconda3/envs/biobakery3/lib/python3.7/subprocess.py”, line 411, in check_output
**kwargs).stdout
File “/Users/****/opt/anaconda3/envs/biobakery3/lib/python3.7/subprocess.py”, line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘bowtie2-build’, ‘–usage’]’ returned non-zero exit status 250.

It appears that my humann couldn’t find the installed metaphlan.

Please let me know how to fix this problem. Many thanks.

Having problem to run the humann3 on our server as well.

nano function.sh

#!/bin/bash
source /local/cluster/humann3/activate.sh

for i in $(ls -1 *fastq ); do
base=${i/_R_cat.fastq/}
echo “i=$i, base=$base”
humann --input $i
–output …/pathways/${base}
–remove-temp-output
–threads 4
–metaphlan /local/cluster/metaphlan3
–nucleotide-database /nfs1/CGRB/databases/humann3\chocophlan
–protein-database /nfs1/CGRB/databases/humann3/uniref
done

[Linux@vaughan merged]$ function1.sh

i=Sample-43_R_cat.fastq, base=Sample-43

Output files will be written to: /raid1/home/pi/lichen/CH4BMFC/pathways/Sample-43

CRITICAL ERROR: Can not call software version for metaphlan

i=Sample-44_R_cat.fastq, base=Sample-44

Output files will be written to: /raid1/home/pi/lichen/CH4BMFC/pathways/Sample-44

CRITICAL ERROR: Can not call software version for metaphlan

i=Sample-45_R_cat.fastq, base=Sample-45

Output files will be written to: /raid1/home/pi/lichen/CH4BMFC/pathways/Sample-45

CRITICAL ERROR: Can not call software version for metaphlan