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