Mykrobe 預測器 AMR 預測不起作用

Question

嘗試在命令行上執行 AMR 預測時收到以下錯誤消息。

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

選擇的物種是結核病 (TB)，而樣本數據文件是從 Mykrobe 網站 ( https://github.com/iqbal-lab/Mykrobe-predictor/releases/download/v0.1.1-beta/demo_input_file_for_M.tuberculosis_app .fastq.gz ）。

以及我收到的錯誤消息...

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

任何建議，將不勝感激。

Answer 1

該錯誤表明缺少mccortex31 。

你是按照文檔安裝的嗎？

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

Answer 2

我是 Mykrobe 預測器的作者之一。 正如上面有人評論的那樣，提出這個問題的正確地點可能是我們 Mykrobe 預測器存儲庫中的 Github 問題：

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

請隨時在那里提出問題。