leylabmpi/Struo2

Cyclic dependency on rule copy_gene_info

yiqijiang17 opened this issue · 2 comments

yiqijiang17 commented

Hi,
I am trying to update the HUMAnN3 with my gene sets which I noticed in another issue.
At the same time, I got an error when I try snakemake --use-conda -j 1 -Fqn, I check the snakefile and think it may be a bug in this function, detailed log:

--Running db-update pipeline--
* Updating genes database
  * Using user-provided set of gene sequences
* Updating humann database
  * Using updated genes database
  * Annotating via "diamond blastp"
CyclicGraphException in line 191 of Struo2/bin/db_update/genes/input/from_gene_set/Snakefile:
Cyclic dependency on rule copy_gene_info.

Yiqi

nick-youngblut commented

@yiqijiang17 I have not been able to reproduce this error. Can you provide some more context?

yiqijiang17 commented

I check again, it was my wrong manipulation. I put the output dir of genes db as the input as I didn't have the amino_acid/nucleotide/metadata of HUMANn3. Thanks for your reply

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