General command line: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/dipspades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C119-dipSPAdes-3.5.0-trimmed

dipSPAdes command line: -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C119-dipSPAdes-3.5.0-trimmed/dipspades --hap /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C119-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta

dipSPAdes parameters:
	K value for dipSPAdes: 55
	Expect gaps: False
	Expect rearrangements: False
	Files with haplocontigs : ['/N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C119-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta']
	Haplotype assembly stage: False
	Output directory: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C119-dipSPAdes-3.5.0-trimmed/dipspades

	Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C119-dipSPAdes-3.5.0-trimmed/dipspades/tmp
	Threads: 16
	Memory limit (in Gb): 250