time /home/reczko/Elixir/metagenomics/minimap2/minimap2-2.17_x64-linux/minimap2 -t 12 -a -d ~/Elixir/metagenomics/SPlab/run440/nt/nt-minimap2-index /data/results/reference/ncbi/nt/nt.gz ~/Elixir/metagenomics/SPlab/mock/Mock_Plant_Community.fastq > ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_Plant_Community.sam

time /home/reczko/Elixir/metagenomics/minimap2/minimap2-2.17_x64-linux/minimap2 -t 12 -a -d ~/Elixir/metagenomics/SPlab/run440/nt/nt-minimap2-index /data/results/reference/ncbi/nt/nt.gz ~/Elixir/metagenomics/SPlab/mock/Mock_others.fastq > ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_others.sam

time /home/reczko/Elixir/metagenomics/minimap2/minimap2-2.17_x64-linux/minimap2 -t 12 -a -d ~/Elixir/metagenomics/SPlab/run440/nt/nt-minimap2-index /data/results/reference/ncbi/nt/nt.gz ~/Elixir/metagenomics/SPlab/mock/Mock_Community_All.fastq > ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_Community_All.sam

cat ~/Elixir/metagenomics/SPlab/run440/nt/head Mock_Plant_Community.sam | samtools view -Sb -  |samtools flagstat -

~/Elixir/metagenomics/megan/megan6/megan/tools/sam2rma
time ~/Elixir/metagenomics/megan/megan6/megan/tools/sam2rma -i ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_Plant_Community.sam  -o  ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_Plant_Community.rma -mdb ~/Elixir/metagenomics/megan/nt/megan-nucl-Oct2019.db
Total reads:       13,495,035
With hits:             555,606 
Alignments:          2,312,020
Assig. Taxonomy:       555,300
MinSupport set to: 6747
Binning reads: Applying min-support & disabled filter to Taxonomy...
Min-supp. changes:       4,136
Binning reads: Writing classification tables
Numb. Tax. classes:         71
Binning reads: Syncing
Class. Taxonomy:            71
100% (503.3s)
Total time:  1319s
Peak memory: 18.1 of 104.9G
real	22m4.150s



time ~/Elixir/metagenomics/megan/megan6/megan/tools/sam2rma -i ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_others.sam  -o  ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_others.rma -mdb ~/Elixir/metagenomics/megan/nt/megan-nucl-Oct2019.db
Total reads:        4,993,314
With hits:             209,375 
Alignments:            855,817
Assig. Taxonomy:       209,090
MinSupport set to: 2496
Binning reads: Applying min-support & disabled filter to Taxonomy...
Min-supp. changes:       2,515
Binning reads: Writing classification tables
Numb. Tax. classes:         87
Binning reads: Syncing
Class. Taxonomy:            87
100% (184.4s)
Total time:  540s
Peak memory: 10.0 of 104.9G
real	9m3.036s



time ~/Elixir/metagenomics/megan/megan6/megan/tools/sam2rma -i ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_Community_All.sam  -o  ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_Community_All.rma -mdb ~/Elixir/metagenomics/megan/nt/megan-nucl-Oct2019.db


time ~/Elixir/metagenomics/megan/megan6/megan/tools/sam2rma -class false -i ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_others.sam  -o  ~/Elixir/metagenomics/SPlab/mock/minimap2/Mock_others_no_classification.rma -mdb ~/Elixir/metagenomics/megan/nt/megan-nucl-Oct2019.db