Yi-Ting Liu Yi-Ting Liu - 1 year ago 108
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
File "/usr/local/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 73, in run
File "/usr/local/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 90, in _run_cortex
File "/usr/local/lib/python2.7/site-packages/mykatlas/cortex/mccortex.py", line 161, in run
File "/usr/local/lib/python2.7/site-packages/mykatlas/cortex/mccortex.py", line 173, in _run_cortex
File "/usr/local/lib/python2.7/site-packages/mykatlas/cortex/mccortex.py", line 190, in _build_panel_binary_if_required
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 Source

The error indicates that mccortex31 is missing.

Did you install it according to the documentation?

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