Issues with getting humann2 to run the example data

From: Weiss, Ken <kgweiss@med.umich.edu>

Greetings,

I am hoping that you can help me to get my installation of humann2 working.

I have bowtie2 version 2.3.4.3 and python 3.6 loaded successfully on my system.

I have tried following the instructions at: https://bitbucket.org/biobakery/humann2/wiki/Home#markdown-header-2-install-humann2 where I clone the repo and then issue: python setup install –user

This installs cleanly and informs me that diamond has been installed as well.

I next run the humann2_test. This also runs successfully.

Next I try the demo run with: humann2 –input examples/demo.fastq --output …

This complains about not being able to find metaphlan.py. I then clone that repo with the command: hg clonehttps://bitbucket.org/biobakery/metaphlan2 and export the metaphlan2 directory onto my $PATH and export mpa_dir=/the/metaphlan2/directory. Running metaphlan2 --version complains about biom format not being available. I then execute: pip install biom-format --user which installs successfully. FYI: metaphlan2 is version 2.7.7

Back to the humann2 demo run and I get the following log:

12/09/2019 03:50:19 PM - humann2.humann2 - INFO: Running humann2 v2.8.1

12/09/2019 03:50:19 PM - humann2.humann2 - INFO: Output files will be written to: /home/kgweiss

12/09/2019 03:50:19 PM - humann2.humann2 - INFO: Writing temp files to directory: /home/kgweiss/demo_humann2_temp

12/09/2019 03:50:19 PM - humann2.utilities - INFO: File ( /home/kgweiss/humann2/examples/demo.fastq ) is of format: fastq

12/09/2019 03:50:19 PM - humann2.utilities - DEBUG: Check software, bowtie2, for required version, 2.2

12/09/2019 03:50:19 PM - humann2.utilities - INFO: Using bowtie2 version 2.3

12/09/2019 03:50:19 PM - humann2.humann2 - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected

12/09/2019 03:50:19 PM - humann2.utilities - DEBUG: Check software, diamond, for required version, 0.8.22

12/09/2019 03:50:19 PM - humann2.utilities - INFO: Using diamond version 0.8.22

12/09/2019 03:50:19 PM - humann2.config - INFO:

Run config settings:

DATABASE SETTINGS

nucleotide database folder = /home/kgweiss/.local/lib/python3.6/site-packages/humann2/data/chocophlan_DEMO

protein database folder = /home/kgweiss/.local/lib/python3.6/site-packages/humann2/data/uniref_DEMO

pathways database file 1 = /home/kgweiss/.local/lib/python3.6/site-packages/humann2/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2

pathways database file 2 = /home/kgweiss/.local/lib/python3.6/site-packages/humann2/data/pathways/metacyc_pathways_structured_filtered

utility mapping database folder = /home/kgweiss/.local/lib/python3.6/site-packages/humann2/data/misc

RUN MODES

resume = False

verbose = False

bypass prescreen = False

bypass nucleotide index = False

bypass nucleotide search = False

bypass translated search = False

translated search = diamond

pick frames = off

threads = 1

SEARCH MODE

search mode = uniref90

identity threshold = 90.0

ALIGNMENT SETTINGS

evalue threshold = 1.0

prescreen threshold = 0.01

translated subject coverage threshold = 50.0

translated query coverage threshold = 90.0

PATHWAYS SETTINGS

minpath = on

xipe = off

gap fill = on

INPUT AND OUTPUT FORMATS

input file format = fastq

output file format = tsv

output max decimals = 10

remove stratified output = False

remove column description output = False

log level = DEBUG

12/09/2019 03:50:19 PM - humann2.store - DEBUG: Initialize Alignments class instance to minimize memory use

12/09/2019 03:50:19 PM - humann2.store - DEBUG: Initialize Reads class instance to minimize memory use

12/09/2019 03:50:25 PM - humann2.humann2 - INFO: Load pathways database part 1: /home/kgweiss/.local/lib/python3.6/site-packages/humann2/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2

12/09/2019 03:50:25 PM - humann2.humann2 - INFO: Load pathways database part 2: /home/kgweiss/.local/lib/python3.6/site-packages/humann2/data/pathways/metacyc_pathways_structured_filtered

12/09/2019 03:50:25 PM - humann2.utilities - DEBUG: Check software, metaphlan2.py, for required version, 2.6

12/09/2019 03:50:25 PM - humann2.utilities - CRITICAL: Can not call software version for metaphlan2.py

Any help you can provide would be greatly appreciated.

Cheers,
Ken Weiss
Health Information Technology Service
University of Michigan
kgweiss@umich.edu

I am having the same issue for the versions of metaphlan2 and humann2 you mentioned.

Did you find any potential solution to this problem?

Regards

Hello Ken, Sorry for the slow response. Can you try running $ metaphlan2.py --version. There is likely an error or message that prevents humann v2 from calling the metaphlan v2 version. If you can resolve that message it should resolve the error you are seeing.

Thank you,
Lauren