Open JWDebler opened 2 weeks ago
Are these two separate augustus
installs? Can you look at the specific build numbers from conda? I'm guess there is an issue with the build version in 1.8.17 install. If BUSCO fails its almost always an Augustus issue....
Yes, they're installed on separate virtual machines, both were setup via conda with what was the latest funannotate version at the time.
The one in the 1.8.15 install: augustus 3.5.0 pl5321hf46c7bb_1 bioconda
The one in the 1.8.17 install: augustus 3.5.0 pl5321h95201ac_4 bioconda
Okay so _4 build is the problem. Force install _1 build and should work.
I just tried that and it complained
mamba install augustus=3.5.0=pl5321hf46c7bb_1
Would this work? mamba install "augustus==3.5.0,!=3.5.0=pl5321h95201ac_4"
In your particular case, you can just install funannotate via pip in your v1.8.15 environment which has a working augustus installation. ie
python -m pip install "funannotate==1.8.17"
Would this work?
mamba install "augustus==3.5.0,!=3.5.0=pl5321h95201ac_4"
The following package could not be installed
└─ augustus ==3.5.0,!=3.5.0 pl5321h95201ac_4 does not exist (perhaps a typo or a missing channel).
That syntax is incorrect.
In your particular case, you can just install funannotate via pip in your v1.8.15 environment which has a working augustus installation. ie
I probably could, but that machine is about to get deleted, which is why I am setting everything up on a new one.
I have tried installing other Augustus builds, but keep running into the same libboost dependency problems. If I remember correctly when I set up this envirionment that was a problem and had to be installed separately after installing funannotate via conda.
I am currently running a few full genomes through the pipeline and everything works fine, it's just the BUSCO validation that returns fewer validated genes than the previous version did.
Frustrating!
You can certainly compile Augustus manually and link it to the conda environment. I actually use a dockerized version locally as none of them will work on apple-silicon..... https://github.com/nextgenusfs/dockerized-augustus. This is hacky but it works, I just put the dockerized scripts in the PATH....
Jumping in here; I've rebuilt augustus
here, could you see if the new Augustus build fixes the issue?
Installed your latest Augustus build, but the test pipeline still fails due to validating too few BUSCO models.
Okay digging into this more. I setup a docker install of funannotate v1.8.17 installed via conda in order to test. What I'm seeing in the filtering step (which extracts the protein sequences and then does an all-vs-all to ensure that all gene calls are more than 80% divergent) is this (which is clearly wrong).
>gene364.t1 gene364
MCGIFAAFKHEDIHNFKPKALQLSKKIRHRGPDWSGNAVMNSTIFVHERLAIVGLDSGAQPITSADGEYMLGVNGEIYNH
IQLREMCSDYKFQTFSDCEPIIPLYLEHDIDAPKYLDGMFAFCLYDSKKDRIVAARDPIGVVTLYMGRSSQSPETVYFAS
ELKCLTDVCDSIISFPPGHVYDSETDKITRYFTPDWLDEKRIPSTPVDYHAIRHSLEKAVRKRLMAEVPYGVLLSGGLDS
SLIAAIAARETEKANADANEDNNVDEKQLAGIDDQGHLHTSGWSRLHSFAIGLPNAPDLQAARKVAKFIGSIHHEHTFTL
QEGLDALDDVIYHLETYDVTTIRASTPMFLLSRKIKAQGVKMVLSGEGSDEIFGGYLYFAQAPSAAEFHTESVQRVKNLH
LADCLRANKSTMAWGLEARVPFLDKDFLQLCMNIDPNEKMIKPKEGRIEKYILRKAFDTTDEPDVKPYLPEEILWRQKEQ
FSDGVGYSWIDGLRDTAERAISDAMFANPKADWGDDIPTTKEAYWYRLKFDAWFPQKTAADTVMRWIPKADWGCAEDPSG
RYAKIHEKHVSA**
>gene365.t1 gene365
N
>gene366.t1 gene366
D
>gene367.t1 gene367
S
>gene368.t1 gene368
MGEKRNRNGKDANSQNRKKFKVSSGFLDPGTSGIYATCSRRHERQAAQELQLLFEEKFQELYGDIKEGEDESENDEKKDL
SIEDQIKKELQELKGEETGKDLSSGETKKKDPLAFIDLNCECVTFCKTRKPIVPEEFVLSIMKDLADPKNMVKRTRYVQK
LTPITYSCNAKMEQLIKLANLVIGPHFHDPSNVKKNYKFAVEVTRRNFNTIERMDIINQVVKLVNKEGSEFNHTVDLKNY
DKLILVECFKSNIGMCVVDGDYKTKYRKYNVQQLYESKFRKDEDKSVKQ**
>gene369.t1 gene369
N
>gene370.t1 gene370
D
Still trying to figure out if related to Augustus build or the other possibility is this is a python 3.8 vs python 3.9 issue, ie in relation to how the code is parsing the Augustus results.
I just installed 1.8.17 on a new system and am going through the test pipeline fixing errors.
The current one though I am not sure what to do about.
It happens during BUSCO-mediated training. However, the same step finishes fine on my old machine with 1.8.15 (below)
1.8.17:
1.8.15:
As can be seen, both versions find the same number of BUSCO predictions (370), but 1.8.17 can only validate 189 of them, crashing the pipeline as AUGUSTUS requires at least 200. 1.8.15 however manages to validate 367.
Versions:
Any suggestions?
Cheers.