Question

尝试在命令行上执行AMR预测时，收到以下错误消息。

mykrobe predict tb_sample_id tb -1 /home/TB/demo_input_file_for_M.tuberculosis_app.fastq

选择的物种是结核病（TB），而样本数据文件是从Mykrobe网站（https://github.com/iqbal-lab/Mykrobe-predictor/releases/download/v0.1.1-beta/demo_input_file_for_M.tuberculosis_app.fastq.gz）下载的。

以及错误消息我正在......

Traceback (most recent call last):
  File "/usr/local/bin/mykrobe", line 9, in <module>
    load_entry_point('mykrobe==0.4.2', 'console_scripts', 'mykrobe')()
  File "/usr/local/lib/python2.7/site-packages/mykrobe/mykrobe_predictor.py", line 99, in main
    args.func(parser, args)
  File "/usr/local/lib/python2.7/site-packages/mykrobe/mykrobe_predictor.py", line 32, in run_subtool
    run(parser, args)
  File "/usr/local/lib/python2.7/site-packages/mykrobe/cmds/amr.py", line 127, in run
    cp.run()
  File "/usr/local/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 73, in run
    self._run_cortex()
  File "/usr/local/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 90, in _run_cortex
    self.mc_cortex_runner.run()
  File "/usr/local/lib/python2.7/site-packages/mykatlas/cortex/mccortex.py", line 161, in run
    self._run_cortex()
  File "/usr/local/lib/python2.7/site-packages/mykatlas/cortex/mccortex.py", line 173, in _run_cortex
    self._build_panel_binary_if_required()
  File "/usr/local/lib/python2.7/site-packages/mykatlas/cortex/mccortex.py", line 190, in _build_panel_binary_if_required
    subprocess.check_output(cmd)
  File "/usr/local/lib/python2.7/subprocess.py", line 566, in check_output
    process = Popen(stdout=PIPE, *popenargs, **kwargs)
  File "/usr/local/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/local/lib/python2.7/subprocess.py", line 1335, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

任何建议都将不胜感激。

Answer 1

错误表示缺少mccortex31。

您是否根据documentation安装了它？

cd Mykrobe-predictor
cd mccortex
make    
export PATH=$PATH:$(pwd)/bin
cd ..

Answer 2

我是Mykrobe预测者的作者之一。正如上面评论过的人，在我们的Mykrobe预测器存储库中，提出这个问题的正确位置可能是一个Github问题：

https://github.com/iqbal-lab/Mykrobe-predictor/issues

请随时提出问题。

Mykrobe预测器AMR预测不起作用

2 个答案: