MaltRun - Aligns sequences using MALT (MEGAN alignment tool)
Options:
Mode:
	--mode: BlastN
	--alignmentType: SemiGlobal
Input:
	--inFile: ...
	--index: /scratch/jneuka/malt/databases/indexed/refseq-genomes-2018_05/
Output:
	--output: results/
	--includeUnaligned: false
	--alignments: results/
	--format: SAM
	--gzipAlignments: false
	--samSoftClip: false
	--sparseSAM: false
Performance:
	--numThreads: 112
	--memoryMode: load
	--maxTables: 0
	--replicateQueryCache: false
Filter:
	--minBitScore: 50.0
	--maxExpected: 1.0
	--minPercentIdentity: 85.0
	--maxAlignmentsPerQuery: 25
	--maxAlignmentsPerRef: 1
BlastN parameters:
	--matchScore: 2
	--mismatchScore: -3
	--setLambda: 0.625
	--setK: 0.41
DNA query parameters:
	--forwardOnly: false
	--reverseOnly: false
LCA parameters:
	--topPercent: 1.0
	--minSupportPercent: 0.001
	--minSupport: 5
	(--minSupportPercent: overridden, set to 0)
	--minPercentIdentityLCA: 0.0
	--useMinPercentIdentityFilterLCA: false
	--weightedLCA: false
	--magnitudes: false
Heuristics:
	--maxSeedsPerFrame: 100
	--maxSeedsPerRef: 20
	--seedShift: 1
Banded alignment parameters:
	--gapOpen: 7
	--gapExtend: 3
	--band: 4
Other:
	--replicateQueryCacheBits: 20
	--xPart: false
	--verbose: true
Version   MALT (version 0.4.1, built 24 May 2018)
Copyright (C) 2018 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.