Getting died with <Signals.SIGKILL: 9> when trying to run Lighter with the human genome size (3.2MB) #36
Description
I'm trying to run this on my computer with a large FASTQ input file, and am running it as a subprocess in Python:
# Set the desired parameters
kmer_size = 31
genome_size = 2000000000
error_rate = 0.1
num_threads = 10
Construct the Lighter command
lighter_command = [
lighter_executable_path,
'-r', input_reads_path,
'-k', str(kmer_size),
str(genome_size),str(error_rate), # Additional arguments
'-t', str(num_threads)
]
However, if I set the genome size any larger than the above, it won't work, as I get the following error message:
line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['../../Lighter/lighter', '-r', '100000_NG1D7PJA9F_1.fq', '-k', '31', '3200000000', '0.1', '-t', '10']' died with <Signals.SIGKILL: 9>.
The README says to put in at least the size of the genome of the organism in question, which in this case is the human genome. Am I doing something wrong that's a simple fix? Thank you!