Problem 1:
Ran the commands:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels biobakery
conda install -c biobakery biobakery_workflows
biobakery_workflows_databases --install wmgx
Got the error:
ImportError: cannot import name ‘complete_to_chordal_graph’ from partially initialized module ‘networkx.algorithms’ (most likely due to a circular import)
Tried to follow the instructions here:
https://forum.biobakery.org/t/biobakery-workflows-wmgx-typeerror/1658/5
The solution suggested was - uninstalling netwrokx and reinstalling it.
In general, uninstalling any package caused me problems as I needed to reinstall biobakery_workflows.
Anyway, that was not the solution for me (didn’t work with any version of networkx).
Solution 1:
Creating a new environment in conda with python 3.7 and not the latest python version which is currently 3.9.
Problem 2:
I downloaded wmgx demo database to try and work on the given example inputs:
biobakery_workflows_databases --install wmgx_demo
biobakery_workflows wmgx --input input --output output_data
Got the error:
task_idxs = nx.algorithms.dag.topological_sort(self.dag, reverse=True)
TypeError: topological_sort() got an unexpected keyword argument ‘reverse’
By this thread’s advice I set networkx to a certain version
Solution 2.a:
conda install networkx=1.11
removing networkx and then reinstalling like this:
conda remove -n huttenhower-py3.7 networkx
conda install networkx=1.11
Forced me to reinstall biobakery_worklflows again:
conda install -c biobakery biobakery_workflows
Ran again the command:
biobakery_workflows wmgx --input input --output output_data
Got the error:
Err: b’ERROR: Unable to find trimmomatic. Please provide the full path to trimmomatic with --trimmomatic.\n’
With the help of this thread figured I needed to point to where trimmoatic*.jar file is after I got another error message like this:
Err: b’ERROR: The trimmomatic*.jar executable is not included in the directory: ~/miniconda3/envs/$MY_ENV/bin/trimmomatic-0.39\n’
Solution 2.b:
Found the location of trimmomatic*.jar:
find -name * trimmomatic*.jar
Then ran the command:
biobakery_workflows wmgx --input input --output output_data --qc-options=“–trimmomatic ~/miniconda3/envs/$MY_ENV/share/trimmomatic-0.39-2/”
Problem 3
After fixing the problems above I ran the command:
biobakery_workflows wmgx --input input --output output_data --qc-options=“–trimmomatic ./miniconda3/envs/$MY_ENV/share/trimmomatic-0.39-2/”
Which brought me to the error message:
Err: b’ERROR: Unable to find bowtie2 index files in directory: ~/biobakery_workflows_databases/kneaddata_db_human_genome\n’
Following kneaddata’s tutorial, I thought of downloading
So I tried downloading the database by doing:
kneaddata_database --download human_genome bowtie2 ~/biobakery_workflows_databases/kneaddata_db_human_genome
My run failed but will update later how I tried to solve the failure.
Err: b’ERROR: You are using the demo ChocoPhlAn database with a non-demo input file. If you have not already done so, please run humann_databases to download the full ChocoPhlAn database. If you have downloaded the full database, use the option --nucleotide-database to provide the location. You can also run humann_config to update the default database location. For additional information, please see the HUMAnN User Manual.\n’
in\nWARNING: Can not call software version for bowtie2\n\n’
Err: b’CRITICAL ERROR: Please update diamond from version 0.9.24 to version 0.9.36\n\n’
I followed this tutorial:
and not this:
I am not yet worried though, as I presume I did not provide the correct input files (I used the files from here) and I need to download more databases. My main issue is problem 4
Problem 4
Meanwhile, I decided to download the full wmgx database.
biobakery_workflows_databases --install wmgx
Got:
error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory
Solution 4.a:
Following this thread, I did:
conda install tbb=2020.2
Ran again:
biobakery_workflows_databases --install wmgx
Got:
Could not locate a Bowtie index corresponding to basename “~/miniconda3/envs/$MY_ENV/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901”
Error: Encountered internal Bowtie 2 exception (#1)
Solution 4.b
Did:
metaphlan --install --bowtie2db $DIR
Even though it was suggested that database should not be put inside the environment, I could not overcome this and had to put it at:
~/miniconda3/envs/$MY_ENV/lib/python3.7/site-packages/metaphlan/metaphlan_databases/
Ran again:
biobakery_workflows_databases --install wmgx
Got the error (when files were being extracted after they were downloaded):
File “~/miniconda3/envs/$MY_ENV/lib/python3.7/http/client.py”, line 292, in _read_status
raise BadStatusLine(line)
http.client.BadStatusLine: -Òì=û)¢ #ÌüE¤VdQ.Ì3Opl«§Ò+inK-n~õãÂFÂjzĤ3©õìV/¡¿I
<ÞQUº\ÙçF{ùÙÓÇ«üÆóß¼U»$ »
¥$
¥¢VVÂ}Mº
Ê®¦·¦èxêßVJC¢§L%`+ûv¹âI ÃÕ;R�«JqÄZéÖÂpå~víúPÝÕÉR+ûáñ¿??|zÂ.
Now this is something I could not overcome alone.
