The dreaded assert vv not in prots2ups assertion error...

[bkr...@ucdavis.edu]

Greetings all,

I'm a new PhytoPhlan user (and commandline newbie...) and am trying to get the program up and running on a local cluster. I managed to get it to work on the test data but have run into common error messages when trying to get it to work with my own sequences. I took care of the "asterisk" issue in my protein sequences but have recently run into the following error.

Traceback (most recent call last):

  File "./phylophlan.py", line 793, in <module>

    gens2prots(inps, projn)

  File "./phylophlan.py", line 311, in gens2prots

    assert vv not in prots2ups

AssertionError

There are several threads dealing with this error which have suggested several causes/solutions including cleaning up files, creating unique headers, and trying new versions of the PhyloPhlan. Cleaning up the files with python phylophlan.py -c "project" did not seem to help so I was going to try to modify my FASTA headers but I'm not sure where to start. I've been unable to find a script online that will work and I'm just starting to learn Python so my programming skills are rudimentary at best. Any help would be greatly appreciated.

Cheers,
Brendan

[Francesco Asnicar]

Hello Brendan,

that error is generally issued when there are conflicting ids in the input fasta files. So, my suggestion is to switch to the "dev" version of PhyloPhlAn. There you can use the new parameter "--faa_cleaning", which take care of producing unique ids in the input fast files provided.

To do this, you simply need to:

 * go to your local directory of PhyloPhlAn cloned from the repository (usually a folder named "phylophlan")

 * execute the following command:

    - $ hg update dev

You have now switched to the "dev" version of PhlyPhlAn. Now, I think that it is better to clean the project folder by typing:

 $ python phylophlan.py -c "project"

Now you can execute the same command you already used (should be something like: $ python phylophlan.py -u "project") with the addition of the "--faa_cleaning" parameter.

Please, let me know if this solve your problem.

Many thanks for using PhyloPhlAn,

Francesco

--
You received this message because you are subscribed to the Google Groups "PhyloPhlAn-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to phylophlan-use...@googlegroups.com.
To post to this group, send email to phylophl...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/12b4a6f6-e41b-4bde-8021-ef945d93c1b4%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Brendan K Riely]

Hi Francesco,

Thanks for getting back to me so promptly! I tried updating PhyloPhlAn and got the following message:

bkriely@farm:~/Rlv_genome_data/sequencing/bin/nsegata-phylophlan-8e2d2ec74872$ hg update dev

abort: no repository found in '/home/bkriely/Rlv_genome_data/sequencing/bin/nsegata-phylophlan-8e2d2ec74872' (.hg not found)!

Am I starting with the wrong version of PhyloPhlAn? Not sure where to go from here. Thanks again for the help.

cheers,
Brendan

---

From: phylophl...@googlegroups.com <phylophl...@googlegroups.com> on behalf of Francesco Asnicar <francesc...@gmail.com>
Sent: Friday, October 7, 2016 11:07:28 AM
To: PhyloPhlAn-users
Subject: Re: The dreaded assert vv not in prots2ups assertion error...

 

You received this message because you are subscribed to a topic in the Google Groups "PhyloPhlAn-users" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/phylophlan-users/qUExjBp7K2c/unsubscribe.
To unsubscribe from this group and all its topics, send an email to phylophlan-use...@googlegroups.com.

To post to this group, send email to phylophl...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/CAORa9gr%3DMPgfaZBVj-ywxiZWLz1Z7FYWFgNeDGjkHeicXQbQvw%40mail.gmail.com.

[Francesco Asnicar]

Hello Brendan,

I think you got that error message because you didn't downloaded PhyloPhlAn as a repository, but from the download page. If that is the case, you just need to type:

 $ hg clone https://bitbucket.org/nsegata/phylophlan
then you can type:

 $ hg update dev

to switch to the "dev" branch.

Please, let me know if you managed to get things working.

Many thanks,
Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/CO2PR0801MB2325D81244257B54BE3FD9C9BDDB0%40CO2PR0801MB2325.namprd08.prod.outlook.com.

[Brendan K Riely]

We're golden! Thanks for the help! BTW, I had to switch to 7.0.1090 to get the program to run. Neither 5.2.32, nor 8.1.1861 would run and I got a

Invalid command line

Option --ublast is invalid

Error. No such problem with usearch 7. Thanks again!

cheers,

b

---

From: phylophl...@googlegroups.com <phylophl...@googlegroups.com> on behalf of Francesco Asnicar <francesc...@gmail.com>

Sent: Monday, October 10, 2016 12:53:29 PM

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/CAORa9gpPDWsXiD9i6sj6sqWpPVbo2zf5gjwPG6R-OZ_F872kMA%40mail.gmail.com.

[Francesco Asnicar]

Great! I'm glad to hear that it worked!

It is strange that the usearch version 8.1.1861 didn't worked... Because is the one that I'm currently using!

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/CO2PR0801MB2325BFE9832D1A0CC8AC19D8BDDA0%40CO2PR0801MB2325.namprd08.prod.outlook.com.

[Caroline Lilliebjörn]

Hello Francesco,

I followed your instructions after receiving the AssertionError with no success. Is there anything else that can be done to fix this error?

Best,

Caroline

[Francesco Asnicar]

Hello Caroline,

Can you provide the full command line and the version of PhyloPhlAn you're using?

Many thanks,

Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/6130ea01-d39a-444e-8e0e-2ed3839b9077%40googlegroups.com.