Yi-Ting Liu Yi-Ting Liu - 2 months ago 23
Linux Question

Mykrobe predictor AMR prediction not working

I am getting the following error message when trying to execute AMR prediction on the command line.

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


The species chosen was Tuberculosis (TB), whereas the sample data file was pulled down from Mykrobe website (https://github.com/iqbal-lab/Mykrobe-predictor/releases/download/v0.1.1-beta/demo_input_file_for_M.tuberculosis_app.fastq.gz).

and the error message I'm getting...

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


Any suggestions would be appreciated.

Answer

The error indicates that mccortex31 is missing.

Did you install it according to the documentation?

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