Request: Default to 1 CPU thread

[schorlton]

Thanks for the great tool. I'm of the opinion that Kleborate should not use more than 1 thread unless allocated more via a command line arg as I suppose it would be possible for it to clobber hundreds of CPUs in a worst case scenario without the user being able to control it.

I see this in the code:

Kleborate/kleborate/kaptive.py

Lines 53 to 68 in f2c9c31

	# Try with multiple threads, and if that fails (possible due to a multithreading BLAST
	# error), try again with one thread.
	kaptive_results = run_kaptive(kaptive_py, kaptive_db, contigs, outfile,
	args.min_kaptive_confidence, one_thread=False)
	if kaptive_results is None:
	kaptive_results = run_kaptive(kaptive_py, kaptive_db, contigs, outfile,
	args.min_kaptive_confidence, one_thread=True)
	assert len(headers) == len(kaptive_results)
	return dict(zip(headers, kaptive_results))
	else:
	return {}
	def run_kaptive(kaptive_py, kaptive_db, contigs, output_file, min_confidence, one_thread):
	thread_option = ' --threads 1' if one_thread else ''

Is it possible limit to 1 thread by default and add a flag when calling the tool if the user wants more? I don't expect that multithreading would provide significant speed advantage regardless?

[WUD2018]

Are there any feedbacks? how can I set the threads used in analysis? thanks