Attribute error when running UPP

[wasade]

Running UPP without arguments yields an AttributeError

$ run_upp.py 
[09:27:49] config.py (line 317):  WARNING: Main configuration file was not found at: /home/mcdonadt/miniconda3/envs/qiime2-2023.5/share/sepp/sepp/upp.config
Proceeding without the main configuration...
[09:27:49] config.py (line 349):     INFO: Seed number: 297834
Traceback (most recent call last):
  File "/home/mcdonadt/miniconda3/envs/qiime2-2023.5/bin/run_upp.py", line 25, in <module>
    main()
  File "/home/mcdonadt/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/sepp/exhaustive_upp.py", line 450, in main
    UPPExhaustiveAlgorithm().run()
  File "/home/mcdonadt/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/sepp/exhaustive_upp.py", line 59, in __init__
    ExhaustiveAlgorithm.__init__(self)
  File "/home/mcdonadt/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/sepp/exhaustive.py", line 236, in __init__
    self.strategy = options().exhaustive.strategy
AttributeError: 'Namespace' object has no attribute 'exhaustive'
(qiime2-2023.5) 09:27:49 (dtmcdonald@b2-001):~$ run_upp.py --version
[09:29:20] config.py (line 317):  WARNING: Main configuration file was not found at: /home/mcdonadt/miniconda3/envs/qiime2-2023.5/share/sepp/sepp/upp.config
Proceeding without the main configuration...
run_upp.py 4.3.10

[smirarab]

Did you run

python setup.py upp

or

python setup.py -c upp

during installation? On my end, I get

python run_upp.py
[16:05:12] config.py (line 370):     INFO: Seed number: 297834
[16:05:12] exhaustive_upp.py (line 185):    ERROR: Either specify the backbone alignment and tree and query sequences or only the query sequences.  Any other combination is invalid

[wasade]

This was from the installation of sepp that comes with QIIME 2, so I'm not sure what's done upstream. @sjanssen2? I think the updates to the bioconda recipe should solve this though

[sjanssen2]

When I came up with the bioconda recipe for SEPP, I never intended to support execution of UPP (I considered UPP a separate software). It was @lrauschning who added config creation of UPP to the bioconda recipe. Besides a run_upp.py --help there doesn't seem to be any functional testing of UPP, so far.

The latest QIIME2 release requires python 3.8 and SEPP 4.3.10 (this conda package was build prior to @lrauschning modifications). Therefore, I recommend adding a subrecipe to bioconda. However, I realized that UPP depends on pasta, which has no functional bioconda package for python 3.8 yet. My attempts to build one fail so far, due to issues with OSX binaries: https://github.com/bioconda/bioconda-recipes/pull/44543. They are not given as dependencies, but downloaded from specific github repos - not very conda like. It might be worth checking if pasta can be build by using conda shipped programs instead?!

[wasade]

cc @dpear

@sjanssen2, any chance you, @dpear, @lrauschning and @yueyujiang could get on a call soon to see if this can all be sorted out?

[yueyujiang]

SEPP or UPP works well when I install them from the source code, but I encountered the same issue when using the bioconda version. I am not sure how to solve this yet.

On Tue, Dec 5, 2023 at 10:01 AM Daniel McDonald @.***> wrote:

cc @dpear https://github.com/dpear

@sjanssen2 https://github.com/sjanssen2, any chance you, @dpear https://github.com/dpear, @lrauschning https://github.com/lrauschning and @yueyujiang https://github.com/yueyujiang could get on a call soon to see if this can all be sorted out?

— Reply to this email directly, view it on GitHub https://github.com/smirarab/sepp/issues/132#issuecomment-1841331914, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKO4576Y3SJFNPUGJ47FCRDYH5OQVAVCNFSM6AAAAAA76D7TA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBRGMZTCOJRGQ . You are receiving this because you were mentioned.Message ID: @.***>

[sjanssen2]

you may want to have a look here: https://github.com/bioconda/bioconda-recipes/pull/44543 Unfortunately, I was not able to find a solution for the raxml option on OSX on bioconda. My local conda builds run through, though.

[sjanssen2]

I am one step closer, as my pasta recipe for bioconda was merged. I am now trying to fix the new sub-recipe (see https://github.com/bioconda/bioconda-recipes/pull/44540) but also the master (see https://github.com/bioconda/bioconda-recipes/pull/44717) recipe build.sh commands to recent changes of the build process.

[wasade]

That's great!!

[sjanssen2]

@wasade and @dpear I could need some help here https://github.com/bioconda/bioconda-recipes/pull/44540 as I don't see the actual blocking error?!

[wasade]

Thanks, @sjanssen2. It looks like the build can't be found (https://dev.azure.com/bioconda/bioconda-recipes/_build/results?buildId=47458&view=logs&j=4ca21543-2a5e-5ae4-2a40-dc36939b1512&t=f4f48d5a-1b26-5059-42bb-482003e0a4ce&l=1460) which is puzzling. I see help output from run_upp.py higher in the result, and an indication of a zero exit status. I wonder if pinging the bioconda devs may be helpful? They've been responsive on Gitter the few times I've needed to inquire

[sjanssen2]

I did not change anything, but now the above issue vanished (must been something on bioconda infrastructure). New recipes have been merged, you should now find py38 and py39 packages for SEPP that should contain proper upp.config files. @wasade let me know if you still have issues.

[wasade]

That's great, thanks!! Can this issue be closed then?

[sjanssen2]

yes. This issue should be closed @smirarab