OK. I tried re-installing using conda only and no pip installs. Oddly, when installing biobakery_workflows via condo it does not install the latest version of AnADAMA2 available in conda. So I updated AnADAMA2 via conda. biobakery_workflows was downgraded when upgrading AnADAMA2. Still get errors. I think Im going to give up using biobakery_workflows 
Here is exactly how I installed, parameters I had to use, and the errors:
$ conda create --yes --name biobakery-conda -c biobakery biobakery_workflows
Must install the database before updating AnADAMA2, else cant install the database.
$ biobakery_workflows_databases --install wmgx
$ conda install anadama2=0.6.7
The following packages will be DOWNGRADED:
biobakery_workflo~ 0.13.2-py27_0 --> 0.13.1-py27_0
$ biobakery_workflows wmgx --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/ --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test2 --grid slurm --grid-jobs 4 --grid-partition NMLResearch --grid-scratch test2/slurm-scratch --threads 8
Error:
ERROR: Unable to find bowtie2 index files in directory: /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_ribosomal_rna
Can get rid of this error by specifying location of database. I think this older version of biobakery_workflows has a bug, it expects to have two databases according to the help page, when there is only one directory.
$ biobakery_workflows wmgx --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/ --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test2 --grid slurm --grid-jobs 4 --grid-partition NMLResearch --grid-scratch test2/slurm-scratch --threads 8 --contaminate-databases /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome
2020-05-12 19:51:39,386 root log_grid_output INFO: Grid 10 from task id standard error:
Downloading MetaPhlAn2 database
Please note due to the size this might take a few minutes
Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v20_m200.tar
Traceback (most recent call last):
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/metaphlan2.py", line 1564, in <module>
metaphlan2()
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/metaphlan2.py", line 1357, in metaphlan2
check_and_install_database(pars['index'], pars['bowtie2db'], pars['bowtie2_build'], pars['nproc'])
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/metaphlan2.py", line 826, in check_and_install_database
download_unpack_tar(DATABASE_DOWNLOAD, index, bowtie2_db, bowtie2_build, nproc)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/metaphlan2.py", line 736, in download_unpack_tar
download(url_tar_file, tar_file)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/metaphlan2.py", line 710, in download
reporthook=ReportHook().report)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 98, in urlretrieve
return opener.retrieve(url, filename, reporthook, data)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 245, in retrieve
fp = self.open(url, data)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 213, in open
return getattr(self, name)(url)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 457, in open_https
return self.http_error(url, fp, errcode, errmsg, headers)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 377, in http_error
result = method(url, fp, errcode, errmsg, headers)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 704, in http_error_401
return getattr(self,name)(url, realm)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 781, in retry_https_basic_auth
user, passwd = self.get_user_passwd(host, realm, i)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 797, in get_user_passwd
user, passwd = self.prompt_user_passwd(host, realm)
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 806, in prompt_user_passwd
host))
EOFError: EOF when reading a line
Task 13 failed
Name: metaphlan2____HSC-10114-HC-01_S15_L001_R1_001
Original error:
Failed to produce target `/Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test2/metaphlan2/main/HSC-10114-HC-01_S15_L001_R1_001_ta
xonomic_profile.tsv'.
biobakery_workflows installed an older version of metaphlan (2.7.7) which still points to the URLs pre-migration. Update to version 2.8.
$ conda install -c bioconda metaphlan2=2.8
It downgraded samtools
samtools 1.10-h9402c20_2 --> 0.1.19-h94a8ba4_6
error
T ask 13 failed
Name: metaphlan2____HSC-10114-HC-01_S15_L001_R1_001
Original error:
Traceback (most recent call last):
File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/wmgx.py", line 174, in <module>
workflow.go()
File "/home/CSCScience.ca/amirza/.local/lib/python2.7/site-packages/anadama2/workflow.py", line 800, in go
self._handle_finished()
File "/home/CSCScience.ca/amirza/.local/lib/python2.7/site-packages/anadama2/workflow.py", line 830, in _handle_finished
self._reporter.finished()
File "/home/CSCScience.ca/amirza/.local/lib/python2.7/site-packages/anadama2/reporters.py", line 218, in finished
r.finished()
File "/home/CSCScience.ca/amirza/.local/lib/python2.7/site-packages/anadama2/reporters.py", line 463, in finished
sys.stdout.write(six.u(" "+print_line+"\n"))
File "/home/CSCScience.ca/amirza/.local/lib/python2.7/site-packages/six.py", line 658, in u
return unicode(s.replace(r'\\', r'\\\\'), "unicode_escape")
TypeError: decoding Unicode is not supported
I thought maybe I should update python
$ conda update python
The following packages will be downloaded:
package | build
---------------------------|-----------------
humann2-2.8.1 | py27_0 61.0 MB bioconda
------------------------------------------------------------
Total: 61.0 MB
The following NEW packages will be INSTALLED:
bmfilter bioconda/linux-64::bmfilter-3.101-hfc679d8_2
bmtagger bioconda/linux-64::bmtagger-3.101-h470a237_4
bmtool bioconda/linux-64::bmtool-3.101-hfc679d8_2
extract_fullseq bioconda/linux-64::extract_fullseq-3.101-3
srprism bioconda/linux-64::srprism-2.4.24-h96824bc_3
trimmomatic bioconda/noarch::trimmomatic-0.39-1
The following packages will be REMOVED:
glpk-4.65-he80fd80_1002
gmp-6.2.0-he1b5a44_2
htslib-1.10.2-h78d89cc_0
java-jdk-8.0.92-1
The following packages will be UPDATED:
kneaddata biobakery/linux-64::kneaddata-0.7.2-p~ --> bioconda/noarch::kneaddata-0.7.4-py_0
libdeflate 1.3-h516909a_0 --> 1.5-h516909a_0
pysam 0.15.3-py27hbcae180_3 --> 0.15.4-py27hbcae180_0
updating python fixed the error but two new errors popped up:
ERROR: Unable to find trimmomatic. Please provide the full path to trimmomatic with --trimmomatic.
Error! numpy python library not detected!!