The bioBakery help forum

16s workflow error

Dear mantainers,
I’d like to use the biobakery workflow to perform my analysis on 16s data.
I’m currently using the Docker container (https://hub.docker.com/r/biobakery/workflows).

However, after (1) downloading the gg references,
wget ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz tar -xf gg_13_8_otus.tar.gz

(2) properly setting the environment variables
export GREEN_GENES_DADA2_DB="./Ref_Biobakery_DB/green_genes_dada2_db"

export GREEN_GENES_FASTA_DB="./Ref_Biobakery_DB/green_genes_dada2_db/99_otus.fasta" # extracted by 'gg_13_8_otus/rep_set_aligned'

export GREEN_GENES_TAXONOMY_DB="./Ref_Biobakery_DB/green_genes_dada2_db/99_otu_taxonomy.txt" # extracted by 'gg_13_8_otus/taxonomy'

and, (3) launching the workflow, I got stuck with this error:

Traceback (most recent call last): File "/usr/local/bin/16s.py", line 182, in <module> workflow.go() File "/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py", line 775, in go task_idxs = nx.algorithms.dag.topological_sort(self.dag, reverse=True) TypeError: topological_sort() got an unexpected keyword argument 'reverse'
How could I solve this issue? I was expected that everything was perfect inside the container.

Thanks in advance,
Mattia

Hello, Thank you for the detailed post! If you update to the latest biobakery workflows docker image or if you update your AnADAMA2 version in your container it should resolve the issue you are seeing. The issue is from a newer version of networkx then was previously compatible with AnADAMA2. We recently updated AnADAMA2 to be compatible with the latest version of networkx.

Thank you,
Lauren