sanger-pathogens/plasmidtron

Assembling the cause of phenotypes and genotypes from NGS data

plasmidtron's Issues

run error of plasmidtron 0.4.1

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When using programs that use GNU Parallel to process data for publication
please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.

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/bin/sh: line 1: 7651 已放弃 kmc_tools -t4 complex traits_config_file > /dev/null 2>&1
Traceback (most recent call last):
File "/hwfssz1/ST_CANCER/CVD/USER/lindechun/software/anaconda2/envs/py3/bin/plasmidtron", line 46, in
plasmid_tron.run()
File "/hwfssz1/ST_CANCER/CVD/USER/lindechun/software/anaconda2/envs/py3/lib/python3.6/site-packages/plasmidtron/PlasmidTron.py", line 244, in run
kmc_complex.run()
File "/hwfssz1/ST_CANCER/CVD/USER/lindechun/software/anaconda2/envs/py3/lib/python3.6/site-packages/plasmidtron/KmcComplex.py", line 113, in run
subprocess.check_call(self.kmc_complex_command('traits_config_file'), shell=True)
File "/hwfssz1/ST_CANCER/CVD/USER/lindechun/software/anaconda2/envs/py3/lib/python3.6/subprocess.py", line 291, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'kmc_tools -t4 complex traits_config_file > /dev/null 2>&1' returned non-zero exit status 134.

Input files for plasmidtron

Hello,
I have installed plasmidtron plus its dependencies as described in the readme file. However, I do not understand what input files should be. specifically, what are file_of_traits and file_of_nontraits?

I have 3 bacteria genomes reads and I would like to pull out the plasmids so that I can study them. How do I format the genomes so that they can satisfy input requirements?

Best regards,
Clabe Wekesa