Closed lmrodriguezr closed 1 month ago
Dear @lmrodriguezr, thank you very much for reporting this and apologies for the frustration.
I find this a bit confusing and I think the error is related to another problem with your anvi'o environment. The error mentions that the prodigal-single-mode
flag is missing in the anvio/__init__.py
, which indeed is not supposed to be there if you are using the stable v8
. As you noted, these changes were made just recently and therefore they should only be present in anvio-dev
branch, so the v8
version of anvi-gen-contigs-database
should not require --prodigal-single-mode
as a potential parameter (but it does, which makes me think that your libraries is from v8
but programs are from anvio-dev
--which can only happen due to some sort of confusion in the anvi'o environment).
I double checked: anvi'o v8
and anvio-dev
branches operate smoothly when I installed them to separate conda environments from scratch. Does this ring a bell? Could it be the case that your environment have files mixed from v8
and anvio-dev
?
One likely solution that would solve this is to install your environment from scratch. I would suggest you to install the development version to track anvio-dev
. If you run into a similar problem we can then quickly address it.
Best wishes, Meren
Hi @meren Thank you! I had replaced the Anvi'o code for the dev version from GitHub in a VM, but I probably missed something in the process. I have now created a fresh Anvi'o environment using conda instead and I no longer have this issue, thank you!
BTW, installing anvio-dev
I encountered this problem: https://github.com/snakemake/snakemake/issues/2607. The solution was very simple, just pip3 install pulp==2.7.0
, so maybe this could be considered in requirements.txt
?
It looks like I'm now facing a different problem, though. CONCOCT is no longer working, and it throws the error:
✖ anvi-cluster-contigs encountered an error after 0:02:25.812512
Config Error: One of the critical output files is missing ('clustering_gt1000.csv'). Please
take a look at the log file: /tmp/tmp14re4_51/logs.txt
Is this a known issue? I'll keep trying :)
Thank you! Miguel.
Oh, never mind, I found this: https://github.com/merenlab/anvio/issues/2154, and I'm now trying agin after pip install scikit-learn==1.1.0
:)
The solution was very simple, just
pip3 install pulp==2.7.0
, so maybe this could be considered inrequirements.txt
?
This is now in the requirements.txt
, @lmrodriguezr! Thank you. If scikit-learn==1.1.0
solves it we should also replace the current scikit==1.2.2
requirement, although I'm not sure whether something will go wrong after that :) Please let us know, and thank you!
scikit=1.2.2
seems to work well, I have not encountered issues with it yet. Thank you @meren !
Short description of the problem
The recently introduced
--prodigal-single-mode
flag from https://github.com/merenlab/anvio/commit/f1291f755c859d55f8152321942f5a62b384676b causes workflows to fail with the following error:Presumably this is because the JSON files are missing the
anvi_gen_contigs_database.--prodigal-single-mode
key, but unfortunately theanvi-run-workflow --get-default-config
command doesn't include it either.I tried the workaround of just adding
anvi_gen_contigs_database.--prodigal-single-mode
manually to the JSON (see the example in the files at the bottom), but that's not recognized:anvi'o version
I'm using the github
HEAD
(this change was introduced 3 weeks ago), but here is the output anyways:System info
Rocky Linux 8.6 (Green Obsidian), using a SIF file with Singularity that I modified to Anvi'o
HEAD
. I cannot use the stable release because of a DAStool issue now solved inHEAD
.Detailed description of the issue
I believe the above (and below) cover all the details, but I'm happy to share the
SIF
if that helps.Files / commands to reproduce the issue
Config files before and after "fix" (which didn't actually fix anything): https://gist.github.com/lmrodriguezr/c60708194da15a1902258e178258afe5