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

Microbial community profiling HUMAnN
1

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.

2

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