MaltRun - Aligns sequences using MALT (MEGAN alignment tool)
Options:
Mode:
        --mode: BlastN
        --alignmentType: Local
Input:
        --inFile: SC-10c-TCMP_S207_L001.unmapped.fasta.gz
        --index: malt_index_megandb
Output:
        --output: test_malt_megandb
        --includeUnaligned: false
        --alignments: test_malt_megandb
        --format: SAM
        --gzipAlignments: true
        --samSoftClip: false
        --sparseSAM: false
Performance:
        --numThreads: 12
        --memoryMode: load
        --maxTables: 0
        --replicateQueryCache: false
Filter:
        --minBitScore: 50.0
        --maxExpected: 1.0E-5
        --minPercentIdentity: 0.0
        --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: 10.0
        --minSupportPercent: 0.001
        --minSupport: 3
        (--minSupportPercent: overridden, set to 0)
        --minPercentIdentityLCA: 95.0
        --useMinPercentIdentityFilterLCA: false   
        --weightedLCA: true
        --lcaCoveragePercent: 80.0
        --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 0.6.1, built 25 Oct 2022) 
Author(s) Daniel H. Huson
Copyright (C) 2022 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
--- LOADING ---:
Reading file: malt_index_megandb/ref.idx
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (0.0s)   
Reading file: malt_index_megandb/ref.db
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (0.3s)   
Number of sequences:        12,420
Number of letters:      16,043,541
LOADING table (0) ...
Reading file: malt_index_megandb/index0.idx
Reference sequence type: DNA
100% (0.0s)
Reading file: malt_index_megandb/table0.idx
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (0.5s)   
Reading file: malt_index_megandb/table0.db
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (0.7s)   
Table size:     15,637,482
Loading ncbi.map: 2,396,736
Loading ncbi.tre: 2,396,740
Reading file: malt_index_megandb/taxonomy.idx
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (0.0s)   
--- ALIGNING ---:
+++++ Aligning file: SC-10c-TCMP_S207_L001.unmapped.fasta.gz
Starting file: test_malt_megandb/SC-10c-TCMP_S207_L001.unmapped.rma6
10% 20% 30% 40% 50% 60% 70% 100% (17.7s)
Alignments written to file: test_malt_megandb/SC-10c-TCMP_S207_L001.unmapped-tmp1001032..blastn..gz
Finishing file: test_malt_megandb/SC-10c-TCMP_S207_L001.unmapped.rma6
Binning reads: Initializing...
Initializing binning...
Computing taxon-to-species map for 'Taxonomy'
Using 'Weighted LCA' assignment (80.0 %) on Taxonomy
Computing weights
Total matches:               0
Total references:            0
Total weights:               0

Binning reads...
Binning reads: Analyzing alignments
Total reads:          106,255
With hits:             106,255
Alignments:          2,230,669
Assig. Taxonomy:             0
Binning reads: Writing classification tables
Numb. Tax. classes:          1
Binning reads: Syncing
Class. Taxonomy:             1
Analysis written to file: test_malt_megandb/SC-10c-TCMP_S207_L001.unmapped.rma6
Prepending @SQ lines to SAM file: test_malt_megandb/SC-10c-TCMP_S207_L001.unmapped.blastn.sam.gz
10% 20% 30% 100% (0.0s)
Copying from temporary file:
100% (8.4s)
Deleted temporary file: test_malt_megandb/SC-10c-TCMP_S207_L001.unmapped-tmp1001032..blastn..gz
Num. of queries:    1153880
Aligned queries:     106255
Num. alignments:    2230669
Total time:  77s
Peak memory: 12.5 of 64G