VIBRANT not working VIBRANT error: could not identify KEGG HMM files in database directory. Please run VIBRANT_setup.py

[Jlee795]

Hi,

I have been trying to use VIBRANT on linux. I installed it through Gitclone as I had trouble trying to install the usual way. I had the message saying vibrant was good to go but when I tried to run it on my data it didn't work. I checked the log and saw this message

"VIBRANT error: could not identify KEGG HMM files in database directory. Please run VIBRANT_setup.py"

I did what it said and ran vibrant set up script and can see the pressed files in the databases folder
e.g.
KEGG_profiles_prokaryotes.HMM
KEGG_profiles_prokaryotes.HMM.h3i
Pfam-A_v32.HMM
Pfam-A_v32.HMM.h3f
Pfam-A_v32.HMM.h3i
Pfam-A_v32.HMM.h3m
Pfam-A_v32.HMM.h3p

VOGDB94_phage.HMM
VOGDB94_phage.HMM.h3f
VOGDB94_phage.HMM.h3i
VOGDB94_phage.HMM.h3m
VOGDB94_phage.HMM.h3p

tried running the command on my own data again and still got the same error message, can anyone advise what to do to fix this please?

Kind Regards,

Jen

[Jlee795]

Hi @KrisKieft is there any ideas with this issue. I saw a closed issue with a solution to this by @BikramDroid. I tried their solution but this hasn't worked for me and I am still not really sure how to sort this.

Any help greatly appreciated,

Kind Regards,

Jlee795

[KrisKieft]

I'm not sure what may have gone wrong but it looks like the database did not fully finish setting up. Can you please try removing KEGG_profiles_prokaryotes.HMM.h3i and then run hmmpress KEGG_profiles_prokaryotes.HMM in the directory where these files are stored.

[Jlee795]

Hi @KrisKieft. This issue has been resolved and Vibrant now runs things. However getting another problem. I was running your mixed example test dataset and had a look at the log file on the github page, your log file says four phages found but when I run the mixed test example dataset my log file says no phages found. Pretty sure that I should get the same output in the log as you get. Do you have any suggestions as to the cause? Any help is greatly appreciated. Thank you,

Kind Regards,

Jlee795

[Jlee795]

This is the output from my log file:

Command: ../VIBRANT_run.py -i mixed_example_1.fasta -t 2 -folder example_test_mixed_3
Date: 2024-04-01
Start: 21:45:12
End: 21:46:18
Runtime: 1.1 minutes
Program: VIBRANT v1.2.1

10 scaffolds were read in.
7 scaffolds met minimum requirements: at least 1000bp and 4 ORFs.
0 putative phages were identified.

CAUTION: running a version of Numpy lower than v1.17.0 will likely cause issues. With pip you can update by running "pip install --upgrade numpy==1.17.0".
##
## ##
## ##

## ## ## ####### ###### ##### ##

## ## ## ## ## ## ## ## ##

###### ###### ## ### ###### ###

## ## ## ## ## ## ## ##

## ## ## ## ####### ###### #####

                                                        #  ##  #
                                                       # # ## # #
                                                      #   #  #   #
                                                     #            #

[Jlee795]

the version of Numpy in my environment is the very version it is mentioning under the caution. So I am not sure as to whether that is the cause. I downloaded VIBRANT as a git clone so it is version 1.2.1

[Jlee795]

@KrisKieft getting this error from the annotation log, which I think the problem of why no phages are found may be related to:

Traceback (most recent call last):
File "/home/crk_w19039039/VIBRANT/databases/VIBRANT/scripts/VIBRANT_annotation.py", line 1422, in
model = pickle.load(read_model)
File "/home/crk_w19039039/.conda/envs/VIBRANT/lib/python3.5/site-packages/numpy/random/_pickle.py", line 2, in
from .philox import Philox
File "philox.pyx", line 1, in init numpy.random.philox
File "init.pxd", line 918, in init numpy.random.bit_generator
ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject

Not really sure how to solve this. any help would be greatly appreciated,

Kind Regards Jlee795

[BioZhang0831]

您好。此问题已解决，Vibrant 现在可以运行。然而，又遇到了另一个问题。我正在运行您的混合示例测试数据集，并查看了 github 页面上的日志文件，您的日志文件显示找到了四个噬菌体，但是当我运行混合测试示例数据集时，我的日志文件显示未找到噬菌体。非常确定我应该在日志中获得与您相同的输出。您对原因有什么建议吗？非常感谢任何帮助。谢谢

亲切问候

杰利795

hello i want to know how you solve this problem to make vibrant run