有没有办法使用 DeepVirFinder 修复此错误代码？

发布于 2025-01-11 14:11:00 字数 1606 浏览 0 评论 0原文

我会尽我所能提供帮助，但这肯定有点超出我的能力范围。

我正在尝试在 Mac 终端内的 fasta 文件“my_seqs.fa”上运行宏基因组学包“DeepVirFinder”。我已按照 GitHub 存储库说明进行操作（如下所示 https://github.com/jessieren/DeepVirFinder ）。我已经创建了一个包含所有必要包的 conda 环境。

在我的终端中，我输入了

python dvf.py -i ~/Documents/PairwiseANI/my_seqs.fna -o ~/Documents/DeepVirFinder/ -l 1000 -c 2

一个来自 GitHub 存储库的输出错误

Using Theano backend.
1. Loading Models.
   model directory /data2/joshcole/DeepVirFinder/models
Traceback (most recent call last):
  File "dvf.py", line 131, in <module>
    modDict[contigLengthk] = load_model(os.path.join(modDir, modName))
  File "/home/ggb_joshcole/miniconda3/envs/dvf/lib/python3.6/site-packages/keras/engine/saving.py", line 419, in load_model
    model = _deserialize_model(f, custom_objects, compile)
  File "/home/ggb_joshcole/miniconda3/envs/dvf/lib/python3.6/site-packages/keras/engine/saving.py", line 224, in _deserialize_model
    model_config = json.loads(model_config.decode('utf-8'))
AttributeError: 'str' object has no attribute 'decode'

，成功运行后应返回的内容（使用示例模板名称）如下：

Using Theano backend.
1. Loading Models.
   model directory /auto/cmb-panasas2/renj/software/DeepVirFinder/models
2. Encoding and Predicting Sequences.
   processing line 1
   processing line 1389
3. Done. Thank you for using DeepVirFinder.
   output in ./test/crAssphage.fa_gt300bp_dvfpred.txt

任何有关如何修复此错误的帮助将不胜感激。我尝试下载并使用潜在的 conda 修复程序进行修复，但这似乎不是任何依赖项的问题+ python 是完全最新的。

感谢您的阅读

原文

I will try to be as much help as I can, but this is certainly a bit out of my depth.

I am trying to run the metagenomics package 'DeepVirFinder' on my fasta file 'my_seqs.fa' within terminal on my Mac. I have followed the GitHub repository instructions (as found here https://github.com/jessieren/DeepVirFinder). I have created a conda environment with all the necessary packages.

Into my terminal I have inputted

python dvf.py -i ~/Documents/PairwiseANI/my_seqs.fna -o ~/Documents/DeepVirFinder/ -l 1000 -c 2

this receives an output error of

Using Theano backend.
1. Loading Models.
   model directory /data2/joshcole/DeepVirFinder/models
Traceback (most recent call last):
  File "dvf.py", line 131, in <module>
    modDict[contigLengthk] = load_model(os.path.join(modDir, modName))
  File "/home/ggb_joshcole/miniconda3/envs/dvf/lib/python3.6/site-packages/keras/engine/saving.py", line 419, in load_model
    model = _deserialize_model(f, custom_objects, compile)
  File "/home/ggb_joshcole/miniconda3/envs/dvf/lib/python3.6/site-packages/keras/engine/saving.py", line 224, in _deserialize_model
    model_config = json.loads(model_config.decode('utf-8'))
AttributeError: 'str' object has no attribute 'decode'

From the GitHub repository, what it should return upon a successful run (using example template names) is as follows:

Using Theano backend.
1. Loading Models.
   model directory /auto/cmb-panasas2/renj/software/DeepVirFinder/models
2. Encoding and Predicting Sequences.
   processing line 1
   processing line 1389
3. Done. Thank you for using DeepVirFinder.
   output in ./test/crAssphage.fa_gt300bp_dvfpred.txt

Any help for how to fix this error would be greatly appreciated. I have tried to download and jig around with potential conda fixes, but it doesn't appear to be a problem with any dependancies + python is fully up to date.

Thank you for reading

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