CAMISIM INSTALLATION Pre-requirements pip install biopython pip install biom pip install matplotlib pip install biom-format git clone https://github.com/CAMI-challenge/CAMISIM pip install scikit-learn==0.22.1 wget https://github.com/bcgsc/NanoSim/releases/download/v2.5.1/NanoSim-v2.5.1.tar.gz /usr/lib/x86_64-linux-gnu sudo ln -s libncursesw.so.6.2 libncursesw.so.5 Genomes to make up community export ref_viruses_rep_genomes=/remote-storage/DBs/blastdb/ref_viruses_rep_genomes blastdbcmd -info -db $ref_viruses_rep_genomes blastdbcmd -db $ref_viruses_rep_genomes -entry 89902998 > ~/CAMISIM/viruses/Ippy01.fasta blastdbcmd -db $ref_viruses_rep_genomes -entry 89902995 > ~/CAMISIM/viruses/Ippy02.fasta blastdbcmd -db $ref_viruses_rep_genomes -entry 9626732 > ~/CAMISIM/viruses/Hepatitis.fasta esearch -db nucleotide -query "AE017125" | efetch -format fasta > CAMISIM/viruses/HelicobacterHepaticus.fasta esearch -db nucleotide -query "NC_007905.1" | efetch -format xml | xtract -pattern Dbtag -element Object-id_id [to obtain the taxon id from NCBI ID] emilio@frodo:~/CAMISIM/viruses$ more virus_metadata.tsv genome_ID OTU NCBI_ID novelty_category Ippy01 1 55096 Ippy virus segment S, complete sequence Ippy02 2 55096 Ippy virus segment L, complete sequence HepatA 3 12092 Hepatitis A virus, complete genome Helico 4 51449 Helicobacter hepaticus ATCC 51449, complete genome emilio@frodo:~/CAMISIM/viruses$ more virus_genome_to_id.tsv Ippy01 /home/emilio/CAMISIM/viruses/genomes/Ippy01.fasta Ippy02 /home/emilio/CAMISIM/viruses/genomes/Ippy02.fasta HepatA /home/emilio/CAMISIM/viruses/genomes/HepatitisA.fasta Helico /home/emilio/CAMISIM/viruses/genomes/HelicobacterHepaticus.fasta Take care of the "community" section in the virus_mini_config.ini to be used running the simulator: emilio@frodo:~/CAMISIM/viruses$ pwd /home/emilio/CAMISIM/viruses emilio@frodo:~/CAMISIM/viruses$ more virus_mini_config.ini ... ... [community0] metadata=viruses/virus_metadata.tsv id_to_genome_file=viruses/virus_genome_to_id.tsv id_to_gff_file= genomes_total=4 genomes_real=4 max_strains_per_otu=1 ratio=1 mode=differential log_mu=1 log_sigma=2 gauss_mu=1 gauss_sigma=1 view=False cd /home/emilio/CAMISIM python metagenomesimulation.py viruses/virus_mini_config.ini OUTPUT: emilio@frodo:~/CAMISIM$ find viruses_out/ -name '*.fq*' viruses_out/2022.04.27_14.20.48_sample_8/reads/anonymous_reads.fq.gz viruses_out/2022.05.17_16.22.21_sample_6/reads/anonymous_reads.fq.gz viruses_out/2022.05.17_16.22.21_sample_1/reads/anonymous_reads.fq.gz viruses_out/2022.04.27_14.20.48_sample_9/reads/anonymous_reads.fq.gz viruses_out/2022.05.17_16.22.21_sample_7/reads/anonymous_reads.fq.gz viruses_out/2022.05.17_16.22.21_sample_8/reads/anonymous_reads.fq.gz viruses_out/2022.05.17_16.22.21_sample_9/reads/anonymous_reads.fq.gz viruses_out/2022.04.27_14.20.48_sample_0/reads/anonymous_reads.fq.gz viruses_out/2022.04.27_14.20.48_sample_4/reads/anonymous_reads.fq.gz viruses_out/2022.04.27_14.20.48_sample_6/reads/anonymous_reads.fq.gz viruses_out/2022.04.27_14.20.48_sample_7/reads/anonymous_reads.fq.gz viruses_out/2022.04.27_14.20.48_sample_2/reads/anonymous_reads.fq.gz viruses_out/2022.04.27_14.20.48_sample_5/reads/anonymous_reads.fq.gz viruses_out/2022.04.27_14.20.48_sample_1/reads/anonymous_reads.fq.gz viruses_out/2022.05.17_16.22.21_sample_2/reads/anonymous_reads.fq.gz viruses_out/2022.05.17_16.22.21_sample_5/reads/anonymous_reads.fq.gz viruses_out/2022.05.17_16.22.21_sample_0/reads/anonymous_reads.fq.gz viruses_out/2022.05.17_16.22.21_sample_4/reads/anonymous_reads.fq.gz viruses_out/2022.05.17_16.22.21_sample_3/reads/anonymous_reads.fq.gz viruses_out/2022.04.27_14.20.48_sample_3/reads/anonymous_reads.fq.gz emilio@frodo:~/CAMISIM$ for i in `ls viruses_out/distributions/*`; do echo $i; cat $i; done viruses_out/distributions/distribution_0.txt Ippy01 0.3987040526398704 Ippy02 0.031414113703141414 HepatA 0.4064039863406404 Helico 0.16347784731634776 viruses_out/distributions/distribution_1.txt Ippy01 0.7517411513 Ippy02 0.2453164702 HepatA 0.0027158048 Helico 0.0002265737 viruses_out/distributions/distribution_2.txt Ippy01 0.2794357968 Ippy02 0.3991007766 HepatA 0.1955179631 Helico 0.1259454635 viruses_out/distributions/distribution_3.txt Ippy01 0.7842071202215792 Ippy02 0.024652630197534737 HepatA 0.13286131698671388 Helico 0.058278932594172106 viruses_out/distributions/distribution_4.txt Ippy01 0.0502694986 Ippy02 0.0283435365 HepatA 0.0240965575 Helico 0.8972904074 viruses_out/distributions/distribution_5.txt Ippy01 0.0629349736 Ippy02 0.1316960549 HepatA 0.2625055309 Helico 0.5428634406 viruses_out/distributions/distribution_6.txt Ippy01 0.061500876 Ippy02 0.0021829334 HepatA 0.0681880139 Helico 0.8681281767 viruses_out/distributions/distribution_7.txt Ippy01 0.2403681192 Ippy02 0.7000444071 HepatA 0.0516847369 Helico 0.0079027368 viruses_out/distributions/distribution_8.txt Ippy01 0.004733904000000001 Ippy02 0.9791927932000001 HepatA 0.015329136200000001 Helico 0.0007441666000000001 viruses_out/distributions/distribution_9.txt Ippy01 0.3264326452 Ippy02 0.0129598746 HepatA 0.1436395253 Helico 0.5169679549 emilio@frodo:~/CAMISIM$ for i in `ls viruses_out/taxonomic*`; do echo $i; cat $i; done viruses_out/taxonomic_profile_0.txt @SampleID: @Version:0.9.1 @Ranks:superkingdom|phylum|class|order|family|genus|species|strain @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE _CAMI_genomeID _CAMI_OTU 10239 superkingdom 10239 Viruses 83.6522 2759 superkingdom 2759 Eukaryota 16.3478 35493 phylum 2759|35493 Eukaryota|Streptophyta 16.3478 4447 class 2759|35493|4447 Eukaryota|Streptophyta|Liliopsida 16.3478 464095 order 10239|||464095 Viruses|||Picornavirales 40.6404 73496 order 2759|35493|4447|73496 Eukaryota|Streptophyta|Liliopsida|Asparagales 16.3478 11617 family 10239||||11617 Viruses||||Arenaviridae 43.0118 12058 family 10239|||464095|12058 Viruses|||Picornavirales|Picornaviridae 40.6404 4668 family 2759|35493|4447|73496|4668 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae 16.3478 1653394 genus 10239||||11617|1653394 Viruses||||Arenaviridae|Mammarenavirus 43.0118 12091 genus 10239|||464095|12058|12091 Viruses|||Picornavirales|Picornaviridae|Hepatovirus 40.6404 51449 genus 2759|35493|4447|73496|4668|51449 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia 16.3478 55096 species 10239||||11617|1653394|55096 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus 43.0118 12092 species 10239|||464095|12058|12091|12092 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A 40.6404 55096.1 strain 10239||||11617|1653394|55096|55096.1 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 39.8704 Ippy01 1 55096.2 strain 10239||||11617|1653394|55096|55096.2 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 3.1414 Ippy02 2 12092.1 strain 10239|||464095|12058|12091|12092|12092.1 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A|Hepatovirus A strain 40.6404 HepatA 3 51449.1 strain 2759|35493|4447|73496|4668|51449||51449.1 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia||Gilliesia strain 16.3478 Helico 4 viruses_out/taxonomic_profile_1.txt @SampleID: @Version:0.9.1 @Ranks:superkingdom|phylum|class|order|family|genus|species|strain @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE _CAMI_genomeID _CAMI_OTU 10239 superkingdom 10239 Viruses 99.9773 2759 superkingdom 2759 Eukaryota 0.0227 35493 phylum 2759|35493 Eukaryota|Streptophyta 0.0227 4447 class 2759|35493|4447 Eukaryota|Streptophyta|Liliopsida 0.0227 464095 order 10239|||464095 Viruses|||Picornavirales 0.2716 73496 order 2759|35493|4447|73496 Eukaryota|Streptophyta|Liliopsida|Asparagales 0.0227 11617 family 10239||||11617 Viruses||||Arenaviridae 99.7058 12058 family 10239|||464095|12058 Viruses|||Picornavirales|Picornaviridae 0.2716 4668 family 2759|35493|4447|73496|4668 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae 0.0227 1653394 genus 10239||||11617|1653394 Viruses||||Arenaviridae|Mammarenavirus 99.7058 12091 genus 10239|||464095|12058|12091 Viruses|||Picornavirales|Picornaviridae|Hepatovirus 0.2716 51449 genus 2759|35493|4447|73496|4668|51449 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia 0.0227 55096 species 10239||||11617|1653394|55096 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus 99.7058 12092 species 10239|||464095|12058|12091|12092 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A 0.2716 55096.1 strain 10239||||11617|1653394|55096|55096.1 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 75.1741 Ippy01 1 55096.2 strain 10239||||11617|1653394|55096|55096.2 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 24.5316 Ippy02 2 12092.1 strain 10239|||464095|12058|12091|12092|12092.1 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A|Hepatovirus A strain 0.2716 HepatA 3 51449.1 strain 2759|35493|4447|73496|4668|51449||51449.1 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia||Gilliesia strain 0.0227 Helico 4 viruses_out/taxonomic_profile_2.txt @SampleID: @Version:0.9.1 @Ranks:superkingdom|phylum|class|order|family|genus|species|strain @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE _CAMI_genomeID _CAMI_OTU 10239 superkingdom 10239 Viruses 87.4055 2759 superkingdom 2759 Eukaryota 12.5945 35493 phylum 2759|35493 Eukaryota|Streptophyta 12.5945 4447 class 2759|35493|4447 Eukaryota|Streptophyta|Liliopsida 12.5945 464095 order 10239|||464095 Viruses|||Picornavirales 19.5518 73496 order 2759|35493|4447|73496 Eukaryota|Streptophyta|Liliopsida|Asparagales 12.5945 11617 family 10239||||11617 Viruses||||Arenaviridae 67.8537 12058 family 10239|||464095|12058 Viruses|||Picornavirales|Picornaviridae 19.5518 4668 family 2759|35493|4447|73496|4668 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae 12.5945 1653394 genus 10239||||11617|1653394 Viruses||||Arenaviridae|Mammarenavirus 67.8537 12091 genus 10239|||464095|12058|12091 Viruses|||Picornavirales|Picornaviridae|Hepatovirus 19.5518 51449 genus 2759|35493|4447|73496|4668|51449 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia 12.5945 55096 species 10239||||11617|1653394|55096 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus 67.8537 12092 species 10239|||464095|12058|12091|12092 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A 19.5518 55096.1 strain 10239||||11617|1653394|55096|55096.1 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 27.9436 Ippy01 1 55096.2 strain 10239||||11617|1653394|55096|55096.2 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 39.9101 Ippy02 2 12092.1 strain 10239|||464095|12058|12091|12092|12092.1 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A|Hepatovirus A strain 19.5518 HepatA 3 51449.1 strain 2759|35493|4447|73496|4668|51449||51449.1 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia||Gilliesia strain 12.5945 Helico 4 viruses_out/taxonomic_profile_3.txt @SampleID: @Version:0.9.1 @Ranks:superkingdom|phylum|class|order|family|genus|species|strain @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE _CAMI_genomeID _CAMI_OTU 10239 superkingdom 10239 Viruses 94.1721 2759 superkingdom 2759 Eukaryota 5.8279 35493 phylum 2759|35493 Eukaryota|Streptophyta 5.8279 4447 class 2759|35493|4447 Eukaryota|Streptophyta|Liliopsida 5.8279 464095 order 10239|||464095 Viruses|||Picornavirales 13.2861 73496 order 2759|35493|4447|73496 Eukaryota|Streptophyta|Liliopsida|Asparagales 5.8279 11617 family 10239||||11617 Viruses||||Arenaviridae 80.8860 12058 family 10239|||464095|12058 Viruses|||Picornavirales|Picornaviridae 13.2861 4668 family 2759|35493|4447|73496|4668 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae 5.8279 1653394 genus 10239||||11617|1653394 Viruses||||Arenaviridae|Mammarenavirus 80.8860 12091 genus 10239|||464095|12058|12091 Viruses|||Picornavirales|Picornaviridae|Hepatovirus 13.2861 51449 genus 2759|35493|4447|73496|4668|51449 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia 5.8279 55096 species 10239||||11617|1653394|55096 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus 80.8860 12092 species 10239|||464095|12058|12091|12092 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A 13.2861 55096.1 strain 10239||||11617|1653394|55096|55096.1 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 78.4207 Ippy01 1 55096.2 strain 10239||||11617|1653394|55096|55096.2 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 2.4653 Ippy02 2 12092.1 strain 10239|||464095|12058|12091|12092|12092.1 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A|Hepatovirus A strain 13.2861 HepatA 3 51449.1 strain 2759|35493|4447|73496|4668|51449||51449.1 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia||Gilliesia strain 5.8279 Helico 4 viruses_out/taxonomic_profile_4.txt @SampleID: @Version:0.9.1 @Ranks:superkingdom|phylum|class|order|family|genus|species|strain @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE _CAMI_genomeID _CAMI_OTU 10239 superkingdom 10239 Viruses 10.2710 2759 superkingdom 2759 Eukaryota 89.7290 35493 phylum 2759|35493 Eukaryota|Streptophyta 89.7290 4447 class 2759|35493|4447 Eukaryota|Streptophyta|Liliopsida 89.7290 464095 order 10239|||464095 Viruses|||Picornavirales 2.4097 73496 order 2759|35493|4447|73496 Eukaryota|Streptophyta|Liliopsida|Asparagales 89.7290 11617 family 10239||||11617 Viruses||||Arenaviridae 7.8613 12058 family 10239|||464095|12058 Viruses|||Picornavirales|Picornaviridae 2.4097 4668 family 2759|35493|4447|73496|4668 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae 89.7290 1653394 genus 10239||||11617|1653394 Viruses||||Arenaviridae|Mammarenavirus 7.8613 12091 genus 10239|||464095|12058|12091 Viruses|||Picornavirales|Picornaviridae|Hepatovirus 2.4097 51449 genus 2759|35493|4447|73496|4668|51449 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia 89.7290 55096 species 10239||||11617|1653394|55096 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus 7.8613 12092 species 10239|||464095|12058|12091|12092 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A 2.4097 55096.1 strain 10239||||11617|1653394|55096|55096.1 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 5.0269 Ippy01 1 55096.2 strain 10239||||11617|1653394|55096|55096.2 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 2.8344 Ippy02 2 12092.1 strain 10239|||464095|12058|12091|12092|12092.1 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A|Hepatovirus A strain 2.4097 HepatA 3 51449.1 strain 2759|35493|4447|73496|4668|51449||51449.1 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia||Gilliesia strain 89.7290 Helico 4 viruses_out/taxonomic_profile_5.txt @SampleID: @Version:0.9.1 @Ranks:superkingdom|phylum|class|order|family|genus|species|strain @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE _CAMI_genomeID _CAMI_OTU 10239 superkingdom 10239 Viruses 45.7137 2759 superkingdom 2759 Eukaryota 54.2863 35493 phylum 2759|35493 Eukaryota|Streptophyta 54.2863 4447 class 2759|35493|4447 Eukaryota|Streptophyta|Liliopsida 54.2863 464095 order 10239|||464095 Viruses|||Picornavirales 26.2506 73496 order 2759|35493|4447|73496 Eukaryota|Streptophyta|Liliopsida|Asparagales 54.2863 11617 family 10239||||11617 Viruses||||Arenaviridae 19.4631 12058 family 10239|||464095|12058 Viruses|||Picornavirales|Picornaviridae 26.2506 4668 family 2759|35493|4447|73496|4668 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae 54.2863 1653394 genus 10239||||11617|1653394 Viruses||||Arenaviridae|Mammarenavirus 19.4631 12091 genus 10239|||464095|12058|12091 Viruses|||Picornavirales|Picornaviridae|Hepatovirus 26.2506 51449 genus 2759|35493|4447|73496|4668|51449 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia 54.2863 55096 species 10239||||11617|1653394|55096 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus 19.4631 12092 species 10239|||464095|12058|12091|12092 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A 26.2506 55096.1 strain 10239||||11617|1653394|55096|55096.1 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 6.2935 Ippy01 1 55096.2 strain 10239||||11617|1653394|55096|55096.2 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 13.1696 Ippy02 2 12092.1 strain 10239|||464095|12058|12091|12092|12092.1 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A|Hepatovirus A strain 26.2506 HepatA 3 51449.1 strain 2759|35493|4447|73496|4668|51449||51449.1 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia||Gilliesia strain 54.2863 Helico 4 viruses_out/taxonomic_profile_6.txt @SampleID: @Version:0.9.1 @Ranks:superkingdom|phylum|class|order|family|genus|species|strain @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE _CAMI_genomeID _CAMI_OTU 10239 superkingdom 10239 Viruses 13.1872 2759 superkingdom 2759 Eukaryota 86.8128 35493 phylum 2759|35493 Eukaryota|Streptophyta 86.8128 4447 class 2759|35493|4447 Eukaryota|Streptophyta|Liliopsida 86.8128 464095 order 10239|||464095 Viruses|||Picornavirales 6.8188 73496 order 2759|35493|4447|73496 Eukaryota|Streptophyta|Liliopsida|Asparagales 86.8128 11617 family 10239||||11617 Viruses||||Arenaviridae 6.3684 12058 family 10239|||464095|12058 Viruses|||Picornavirales|Picornaviridae 6.8188 4668 family 2759|35493|4447|73496|4668 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae 86.8128 1653394 genus 10239||||11617|1653394 Viruses||||Arenaviridae|Mammarenavirus 6.3684 12091 genus 10239|||464095|12058|12091 Viruses|||Picornavirales|Picornaviridae|Hepatovirus 6.8188 51449 genus 2759|35493|4447|73496|4668|51449 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia 86.8128 55096 species 10239||||11617|1653394|55096 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus 6.3684 12092 species 10239|||464095|12058|12091|12092 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A 6.8188 55096.1 strain 10239||||11617|1653394|55096|55096.1 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 6.1501 Ippy01 1 55096.2 strain 10239||||11617|1653394|55096|55096.2 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 0.2183 Ippy02 2 12092.1 strain 10239|||464095|12058|12091|12092|12092.1 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A|Hepatovirus A strain 6.8188 HepatA 3 51449.1 strain 2759|35493|4447|73496|4668|51449||51449.1 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia||Gilliesia strain 86.8128 Helico 4 viruses_out/taxonomic_profile_7.txt @SampleID: @Version:0.9.1 @Ranks:superkingdom|phylum|class|order|family|genus|species|strain @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE _CAMI_genomeID _CAMI_OTU 10239 superkingdom 10239 Viruses 99.2097 2759 superkingdom 2759 Eukaryota 0.7903 35493 phylum 2759|35493 Eukaryota|Streptophyta 0.7903 4447 class 2759|35493|4447 Eukaryota|Streptophyta|Liliopsida 0.7903 464095 order 10239|||464095 Viruses|||Picornavirales 5.1685 73496 order 2759|35493|4447|73496 Eukaryota|Streptophyta|Liliopsida|Asparagales 0.7903 11617 family 10239||||11617 Viruses||||Arenaviridae 94.0413 12058 family 10239|||464095|12058 Viruses|||Picornavirales|Picornaviridae 5.1685 4668 family 2759|35493|4447|73496|4668 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae 0.7903 1653394 genus 10239||||11617|1653394 Viruses||||Arenaviridae|Mammarenavirus 94.0413 12091 genus 10239|||464095|12058|12091 Viruses|||Picornavirales|Picornaviridae|Hepatovirus 5.1685 51449 genus 2759|35493|4447|73496|4668|51449 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia 0.7903 55096 species 10239||||11617|1653394|55096 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus 94.0413 12092 species 10239|||464095|12058|12091|12092 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A 5.1685 55096.1 strain 10239||||11617|1653394|55096|55096.1 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 24.0368 Ippy01 1 55096.2 strain 10239||||11617|1653394|55096|55096.2 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 70.0044 Ippy02 2 12092.1 strain 10239|||464095|12058|12091|12092|12092.1 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A|Hepatovirus A strain 5.1685 HepatA 3 51449.1 strain 2759|35493|4447|73496|4668|51449||51449.1 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia||Gilliesia strain 0.7903 Helico 4 viruses_out/taxonomic_profile_8.txt @SampleID: @Version:0.9.1 @Ranks:superkingdom|phylum|class|order|family|genus|species|strain @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE _CAMI_genomeID _CAMI_OTU 10239 superkingdom 10239 Viruses 99.9256 2759 superkingdom 2759 Eukaryota 0.0744 35493 phylum 2759|35493 Eukaryota|Streptophyta 0.0744 4447 class 2759|35493|4447 Eukaryota|Streptophyta|Liliopsida 0.0744 464095 order 10239|||464095 Viruses|||Picornavirales 1.5329 73496 order 2759|35493|4447|73496 Eukaryota|Streptophyta|Liliopsida|Asparagales 0.0744 11617 family 10239||||11617 Viruses||||Arenaviridae 98.3927 12058 family 10239|||464095|12058 Viruses|||Picornavirales|Picornaviridae 1.5329 4668 family 2759|35493|4447|73496|4668 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae 0.0744 1653394 genus 10239||||11617|1653394 Viruses||||Arenaviridae|Mammarenavirus 98.3927 12091 genus 10239|||464095|12058|12091 Viruses|||Picornavirales|Picornaviridae|Hepatovirus 1.5329 51449 genus 2759|35493|4447|73496|4668|51449 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia 0.0744 55096 species 10239||||11617|1653394|55096 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus 98.3927 12092 species 10239|||464095|12058|12091|12092 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A 1.5329 55096.1 strain 10239||||11617|1653394|55096|55096.1 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 0.4734 Ippy01 1 55096.2 strain 10239||||11617|1653394|55096|55096.2 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 97.9193 Ippy02 2 12092.1 strain 10239|||464095|12058|12091|12092|12092.1 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A|Hepatovirus A strain 1.5329 HepatA 3 51449.1 strain 2759|35493|4447|73496|4668|51449||51449.1 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia||Gilliesia strain 0.0744 Helico 4 viruses_out/taxonomic_profile_9.txt @SampleID: @Version:0.9.1 @Ranks:superkingdom|phylum|class|order|family|genus|species|strain @@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE _CAMI_genomeID _CAMI_OTU 10239 superkingdom 10239 Viruses 48.3032 2759 superkingdom 2759 Eukaryota 51.6968 35493 phylum 2759|35493 Eukaryota|Streptophyta 51.6968 4447 class 2759|35493|4447 Eukaryota|Streptophyta|Liliopsida 51.6968 464095 order 10239|||464095 Viruses|||Picornavirales 14.3640 73496 order 2759|35493|4447|73496 Eukaryota|Streptophyta|Liliopsida|Asparagales 51.6968 11617 family 10239||||11617 Viruses||||Arenaviridae 33.9393 12058 family 10239|||464095|12058 Viruses|||Picornavirales|Picornaviridae 14.3640 4668 family 2759|35493|4447|73496|4668 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae 51.6968 1653394 genus 10239||||11617|1653394 Viruses||||Arenaviridae|Mammarenavirus 33.9393 12091 genus 10239|||464095|12058|12091 Viruses|||Picornavirales|Picornaviridae|Hepatovirus 14.3640 51449 genus 2759|35493|4447|73496|4668|51449 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia 51.6968 55096 species 10239||||11617|1653394|55096 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus 33.9393 12092 species 10239|||464095|12058|12091|12092 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A 14.3640 55096.1 strain 10239||||11617|1653394|55096|55096.1 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 32.6433 Ippy01 1 55096.2 strain 10239||||11617|1653394|55096|55096.2 Viruses||||Arenaviridae|Mammarenavirus|Ippy mammarenavirus|Ippy mammarenavirus strain 1.2960 Ippy02 2 12092.1 strain 10239|||464095|12058|12091|12092|12092.1 Viruses|||Picornavirales|Picornaviridae|Hepatovirus|Hepatovirus A|Hepatovirus A strain 14.3640 HepatA 3 51449.1 strain 2759|35493|4447|73496|4668|51449||51449.1 Eukaryota|Streptophyta|Liliopsida|Asparagales|Amaryllidaceae|Gilliesia||Gilliesia strain 51.6968 Helico 4 Execute the following command to split the fastq.gz file being used in the pipeline seqkit split2 -p2 anonymous_reads.fq.gz --force cd ~/CAMISIM/viruses_out/2022.05.17_16.22.21_sample_9/reads/anonymous_reads.fq.gz.split mv anonymous_reads.part_001.fq.gz sample9_1.fq.gz mv anonymous_reads.part_002.fq.gz sample9_2.fq.gz Run PIMGAVir pipeline using sample9_1.fq.gz and sample9_2.fq.gz as input files. NB.: it is suggested to create a new folder for each execution of PIMGAVir, in order to keep separated the results of each execution) mkdir -p SimulatedData/sample09 mv sample9_1.fq.gz sample9_2.fq.gz SimulatedData cd SimulatedData/sample09 time pimgavir.sh sample9_1.fq.gz sample9_2.fq.gz S09 16 ALL --filter The reported command will execute the 3 strategies in parallel [--read_based, --ass_based, --clust_based] with the filtering option. At the end of the execution, the user will found the folder structure similar to the next one: pimgavir@frodo:~/SimulatedData/sample09$ tree . ├── anonymous_reads.fq ├── anonymous_reads_R1.fq.gz ├── anonymous_reads_R1.fq.gz_trimming_report.txt ├── anonymous_reads_R1_val_1_fastqc.html ├── anonymous_reads_R1_val_1_fastqc.zip ├── anonymous_reads_R2.fq.gz ├── anonymous_reads_R2.fq.gz_trimming_report.txt ├── anonymous_reads_R2_val_2_fastqc.html ├── anonymous_reads_R2_val_2_fastqc.zip ├── assembly-based │   ├── IDXs │   │   ├── megahit_contigs_idx.1.bt2 │   │   ├── megahit_contigs_idx.2.bt2 │   │   ├── megahit_contigs_idx.3.bt2 │   │   ├── megahit_contigs_idx.4.bt2 │   │   ├── megahit_contigs_idx.rev.1.bt2 │   │   ├── megahit_contigs_idx.rev.2.bt2 │   │   ├── spades_contigs_idx.1.bt2 │   │   ├── spades_contigs_idx.2.bt2 │   │   ├── spades_contigs_idx.3.bt2 │   │   ├── spades_contigs_idx.4.bt2 │   │   ├── spades_contigs_idx.rev.1.bt2 │   │   └── spades_contigs_idx.rev.2.bt2 │   ├── megahit_contigs.bam │   ├── megahit_contigs_improved.fasta │   ├── megahit_contigs_improved.fasta.fasta │   ├── megahit_contigs.sorted.bam │   ├── megahit_contigs.sorted.bam.bai │   ├── megahit_data │   │   ├── checkpoints.txt │   │   ├── done │   │   ├── final.contigs.fa │   │   ├── intermediate_contigs │   │   │   ├── k21.addi.fa │   │   │   ├── k21.addi.fa.info │   │   │   ├── k21.bubble_seq.fa │   │   │   ├── k21.bubble_seq.fa.info │   │   │   ├── k21.contigs.fa │   │   │   ├── k21.contigs.fa.info │   │   │   ├── k21.final.contigs.fa │   │   │   ├── k21.final.contigs.fa.info │   │   │   ├── k21.local.fa │   │   │   ├── k21.local.fa.info │   │   │   ├── k41.addi.fa │   │   │   ├── k41.addi.fa.info │   │   │   ├── k41.bubble_seq.fa │   │   │   ├── k41.bubble_seq.fa.info │   │   │   ├── k41.contigs.fa │   │   │   ├── k41.contigs.fa.info │   │   │   ├── k41.final.contigs.fa │   │   │   ├── k41.final.contigs.fa.info │   │   │   ├── k41.local.fa │   │   │   └── k41.local.fa.info │   │   ├── log │   │   └── options.json │   ├── megahit_prokka │   │   ├── megahit_prokka.err │   │   ├── megahit_prokka.faa │   │   ├── megahit_prokka.ffn │   │   ├── megahit_prokka.fna │   │   ├── megahit_prokka.fsa │   │   ├── megahit_prokka.gbk │   │   ├── megahit_prokka.gff │   │   ├── megahit_prokka.log │   │   ├── megahit_prokka.sqn │   │   ├── megahit_prokka.tbl │   │   ├── megahit_prokka.tsv │   │   └── megahit_prokka.txt │   ├── megahit_quast │   │   ├── basic_stats │   │   ├── icarus.html │   │   ├── icarus_viewers │   │   │   └── contig_size_viewer.html │   │   ├── quast.log │   │   ├── report.html │   │   ├── report.tex │   │   ├── report.tsv │   │   ├── report.txt │   │   ├── transposed_report.tex │   │   ├── transposed_report.tsv │   │   └── transposed_report.txt │   ├── spades_contigs.bam │   ├── spades_contigs_improved.fasta │   ├── spades_contigs_improved.fasta.fasta │   ├── spades_contigs.sorted.bam │   ├── spades_contigs.sorted.bam.bai │   ├── spades_data │   │   ├── assembly_graph_after_simplification.gfa │   │   ├── assembly_graph.fastg │   │   ├── assembly_graph_with_scaffolds.gfa │   │   ├── before_rr.fasta │   │   ├── contigs.fasta │   │   ├── contigs.paths │   │   ├── corrected │   │   │   ├── configs │   │   │   │   └── config.info │   │   │   ├── corrected.yaml │   │   │   ├── Forward.00.0_0.cor.fastq.gz │   │   │   ├── Reverse.00.0_0.cor.fastq.gz │   │   │   └── _unpaired.00.0_0.cor.fastq.gz │   │   ├── dataset.info │   │   ├── first_pe_contigs.fasta │   │   ├── input_dataset.yaml │   │   ├── K21 │   │   │   ├── configs │   │   │   │   ├── careful_mda_mode.info │   │   │   │   ├── careful_mode.info │   │   │   │   ├── config.info │   │   │   │   ├── construction.info │   │   │   │   ├── detail_info_printer.info │   │   │   │   ├── distance_estimation.info │   │   │   │   ├── hmm_mode.info │   │   │   │   ├── isolate_mode.info │   │   │   │   ├── large_genome_mode.info │   │   │   │   ├── mda_mode.info │   │   │   │   ├── meta_mode.info │   │   │   │   ├── metaplasmid_mode.info │   │   │   │   ├── metaviral_mode.info │   │   │   │   ├── moleculo_mode.info │   │   │   │   ├── pe_params.info │   │   │   │   ├── plasmid_mode.info │   │   │   │   ├── rna_mode.info │   │   │   │   ├── rnaviral_mode.info │   │   │   │   ├── simplification.info │   │   │   │   ├── toy.info │   │   │   │   └── tsa.info │   │   │   ├── final.lib_data │   │   │   └── simplified_contigs │   │   │   ├── contigs_info │   │   │   ├── contigs.off │   │   │   └── contigs.seq │   │   ├── K33 │   │   │   ├── configs │   │   │   │   ├── careful_mda_mode.info │   │   │   │   ├── careful_mode.info │   │   │   │   ├── config.info │   │   │   │   ├── construction.info │   │   │   │   ├── detail_info_printer.info │   │   │   │   ├── distance_estimation.info │   │   │   │   ├── hmm_mode.info │   │   │   │   ├── isolate_mode.info │   │   │   │   ├── large_genome_mode.info │   │   │   │   ├── mda_mode.info │   │   │   │   ├── meta_mode.info │   │   │   │   ├── metaplasmid_mode.info │   │   │   │   ├── metaviral_mode.info │   │   │   │   ├── moleculo_mode.info │   │   │   │   ├── pe_params.info │   │   │   │   ├── plasmid_mode.info │   │   │   │   ├── rna_mode.info │   │   │   │   ├── rnaviral_mode.info │   │   │   │   ├── simplification.info │   │   │   │   ├── toy.info │   │   │   │   └── tsa.info │   │   │   ├── final.lib_data │   │   │   └── simplified_contigs │   │   │   ├── contigs_info │   │   │   ├── contigs.off │   │   │   └── contigs.seq │   │   ├── K55 │   │   │   ├── assembly_graph_after_simplification.gfa │   │   │   ├── assembly_graph.fastg │   │   │   ├── assembly_graph_with_scaffolds.gfa │   │   │   ├── before_rr.fasta │   │   │   ├── configs │   │   │   │   ├── careful_mda_mode.info │   │   │   │   ├── careful_mode.info │   │   │   │   ├── config.info │   │   │   │   ├── construction.info │   │   │   │   ├── detail_info_printer.info │   │   │   │   ├── distance_estimation.info │   │   │   │   ├── hmm_mode.info │   │   │   │   ├── isolate_mode.info │   │   │   │   ├── large_genome_mode.info │   │   │   │   ├── mda_mode.info │   │   │   │   ├── meta_mode.info │   │   │   │   ├── metaplasmid_mode.info │   │   │   │   ├── metaviral_mode.info │   │   │   │   ├── moleculo_mode.info │   │   │   │   ├── pe_params.info │   │   │   │   ├── plasmid_mode.info │   │   │   │   ├── rna_mode.info │   │   │   │   ├── rnaviral_mode.info │   │   │   │   ├── simplification.info │   │   │   │   ├── toy.info │   │   │   │   └── tsa.info │   │   │   ├── final_contigs.fasta │   │   │   ├── final_contigs.paths │   │   │   ├── final.lib_data │   │   │   ├── first_pe_contigs.fasta │   │   │   ├── path_extend │   │   │   ├── scaffolds.fasta │   │   │   ├── scaffolds.paths │   │   │   └── strain_graph.gfa │   │   ├── misc │   │   ├── params.txt │   │   ├── pipeline_state │   │   │   ├── stage_0_before_start │   │   │   ├── stage_10_as_finish │   │   │   ├── stage_11_bs │   │   │   ├── stage_12_terminate │   │   │   ├── stage_1_ec_start │   │   │   ├── stage_2_ec_runtool │   │   │   ├── stage_3_ec_compress │   │   │   ├── stage_4_ec_finish │   │   │   ├── stage_5_as_start │   │   │   ├── stage_6_k21 │   │   │   ├── stage_7_k33 │   │   │   ├── stage_8_k55 │   │   │   └── stage_9_copy_files │   │   ├── run_spades.sh │   │   ├── run_spades.yaml │   │   ├── scaffolds.fasta │   │   ├── scaffolds.paths │   │   ├── spades.log │   │   ├── strain_graph.gfa │   │   ├── tmp │   │   └── warnings.log │   ├── spades_prokka │   │   ├── spades_prokka.err │   │   ├── spades_prokka.faa │   │   ├── spades_prokka.ffn │   │   ├── spades_prokka.fna │   │   ├── spades_prokka.fsa │   │   ├── spades_prokka.gbk │   │   ├── spades_prokka.gff │   │   ├── spades_prokka.log │   │   ├── spades_prokka.sqn │   │   ├── spades_prokka.tbl │   │   ├── spades_prokka.tsv │   │   └── spades_prokka.txt │   └── spades_quast │   ├── basic_stats │   ├── icarus.html │   ├── icarus_viewers │   │   └── contig_size_viewer.html │   ├── quast.log │   ├── report.html │   ├── report.tex │   ├── report.tsv │   ├── report.txt │   ├── transposed_report.tex │   ├── transposed_report.tsv │   └── transposed_report.txt ├── assembly-based.log ├── assembly-based-MEGAHIT-KRONA-BLAST │   ├── blastn.out │   ├── krona-blast.log │   ├── krona_out.html │   ├── krona_stderr │   ├── krona_stdout │   └── krona_tax.lst ├── assembly-based-SPADES-KRONA-BLAST │   ├── blastn.out │   ├── krona-blast.log │   ├── krona_out.html │   ├── krona_stderr │   ├── krona_stdout │   └── krona_tax.lst ├── assembly-based-taxonomy │   ├── krakViral_class.out_MEGAHIT │   ├── krakViral_class.out_SPADES │   ├── krakViral.krona.html_MEGAHIT │   ├── krakViral.krona.html_SPADES │   ├── krakViral.krona_MEGAHIT │   ├── krakViral.krona_SPADES │   ├── krakViral.out_MEGAHIT │   ├── krakViral.out_SPADES │   ├── krakViral_report.out_MEGAHIT │   ├── krakViral_report.out_SPADES │   ├── krakViral_unclass.out_MEGAHIT │   ├── krakViral_unclass.out_SPADES │   ├── reads_kaiju.krona_MEGAHIT │   ├── reads_kaiju.krona_SPADES │   ├── reads_kaiju.kron.html_MEGAHIT │   ├── reads_kaiju.kron.html_SPADES │   ├── readskaiju.out_MEGAHIT │   └── readskaiju.out_SPADES ├── blastx_diamond.m8 ├── blastx_diamond_NoDup.m8 ├── blastx_diamond_NoDup_wanted.m8 ├── blastx_diamond_NoDup_withTaxa.m8 ├── blastx_diamond_NoDup_withTaxa_wanted.m8 ├── clustering-based │   ├── otus.fasta │   └── readsNotrRNA_filtered.fq.split │   ├── clustered.uc │   ├── clustering-based.log │   ├── Combined.fasta │   ├── combined.uc │   ├── concatenate_reads.py │   ├── derep.fasta │   ├── derep_Forward.fasta │   ├── derep_Reverse.fasta │   ├── Forward.fasta │   ├── Forward.uc │   ├── MSA.fa │   ├── nonchimeras.fasta │   ├── otu.biom │   ├── otutab.txt │   ├── preclustered.fasta │   ├── readsNotrRNA_filtered.part_001.fq │   ├── readsNotrRNA_filtered.part_002.fq │   ├── Reverse.fasta │   └── Reverse.uc ├── clustering-based-KRONA-BLAST │   ├── blastn.out │   ├── krona-blast.log │   ├── krona_out.html │   ├── krona_out.html.files │   │   ├── enable.js │   │   ├── node105.members.0.js │   │   ├── node106.members.0.js │   │   ├── node109.members.0.js │   │   ├── node113.members.0.js │   │   ├── node115.members.0.js │   │   ├── node121.members.0.js │   │   ├── node127.members.0.js │   │   ├── node130.members.0.js │   │   ├── node134.members.0.js │   │   ├── node141.members.0.js │   │   ├── node146.members.0.js │   │   ├── node154.members.0.js │   │   ├── node159.members.0.js │   │   ├── node162.members.0.js │   │   ├── node166.members.0.js │   │   ├── node167.members.0.js │   │   ├── node168.members.0.js │   │   ├── node169.members.0.js │   │   ├── node16.members.0.js │   │   ├── node171.members.0.js │   │   ├── node175.members.0.js │   │   ├── node179.members.0.js │   │   ├── node182.members.0.js │   │   ├── node185.members.0.js │   │   ├── node190.members.0.js │   │   ├── node20.members.0.js │   │   ├── node22.members.0.js │   │   ├── node24.members.0.js │   │   ├── node26.members.0.js │   │   ├── node27.members.0.js │   │   ├── node28.members.0.js │   │   ├── node30.members.0.js │   │   ├── node31.members.0.js │   │   ├── node32.members.0.js │   │   ├── node33.members.0.js │   │   ├── node35.members.0.js │   │   ├── node36.members.0.js │   │   ├── node37.members.0.js │   │   ├── node39.members.0.js │   │   ├── node40.members.0.js │   │   ├── node41.members.0.js │   │   ├── node42.members.0.js │   │   ├── node43.members.0.js │   │   ├── node44.members.0.js │   │   ├── node45.members.0.js │   │   ├── node46.members.0.js │   │   ├── node47.members.0.js │   │   ├── node49.members.0.js │   │   ├── node4.members.0.js │   │   ├── node50.members.0.js │   │   ├── node51.members.0.js │   │   ├── node53.members.0.js │   │   ├── node54.members.0.js │   │   ├── node55.members.0.js │   │   ├── node56.members.0.js │   │   ├── node58.members.0.js │   │   ├── node59.members.0.js │   │   ├── node60.members.0.js │   │   ├── node61.members.0.js │   │   ├── node63.members.0.js │   │   ├── node64.members.0.js │   │   ├── node65.members.0.js │   │   ├── node66.members.0.js │   │   ├── node67.members.0.js │   │   ├── node68.members.0.js │   │   ├── node69.members.0.js │   │   ├── node6.members.0.js │   │   ├── node71.members.0.js │   │   ├── node75.members.0.js │   │   ├── node80.members.0.js │   │   ├── node86.members.0.js │   │   ├── node93.members.0.js │   │   └── node96.members.0.js │   ├── krona_stderr │   ├── krona_stdout │   └── krona_tax.lst ├── clustering-based.log ├── clustering-based-taxonomy │   ├── krakViral_class.out_OTU │   ├── krakViral.krona.html_OTU │   ├── krakViral.krona.html_OTU.files │   │   ├── enable.js │   │   ├── node10.members.0.js │   │   ├── node16.members.0.js │   │   ├── node17.members.0.js │   │   ├── node18.members.0.js │   │   ├── node19.members.0.js │   │   ├── node1.members.0.js │   │   ├── node20.members.0.js │   │   ├── node21.members.0.js │   │   ├── node23.members.0.js │   │   ├── node29.members.0.js │   │   ├── node35.members.0.js │   │   ├── node45.members.0.js │   │   ├── node52.members.0.js │   │   ├── node56.members.0.js │   │   ├── node57.members.0.js │   │   └── node6.members.0.js │   ├── krakViral.krona_OTU │   ├── krakViral.out_OTU │   ├── krakViral_report.out_OTU │   ├── krakViral_unclass.out_OTU │   ├── reads_kaiju.krona_OTU │   ├── reads_kaiju.kron.html_OTU │   └── readskaiju.out_OTU ├── diamond.log ├── mega_quast │   ├── basic_stats │   ├── icarus.html │   ├── icarus_viewers │   │   └── contig_size_viewer.html │   ├── quast.log │   ├── report.html │   ├── report.tex │   ├── report.tsv │   ├── report.txt │   ├── transposed_report.tex │   ├── transposed_report.tsv │   └── transposed_report.txt ├── Misaele_Filter_Param.log ├── NoDup.taxonomy.krona.html ├── pimgavir.log ├── pre-process.log ├── read-based-KRONA-BLAST │   ├── blastn.out │   ├── krona-blast.log │   ├── krona_out.html │   ├── krona_out.html.files │   │   ├── enable.js │   │   ├── node100.members.0.js │   │   ├── node102.members.0.js │   │   ├── node104.members.0.js │   │   ├── node106.members.0.js │   │   ├── node107.members.0.js │   │   ├── node108.members.0.js │   │   ├── node109.members.0.js │   │   ├── node10.members.0.js │   │   ├── node110.members.0.js │   │   ├── node111.members.0.js │   │   ├── node112.members.0.js │   │   ├── node113.members.0.js │   │   ├── node114.members.0.js │   │   ├── node115.members.0.js │   │   ├── node116.members.0.js │   │   ├── node117.members.0.js │   │   ├── node118.members.0.js │   │   ├── node119.members.0.js │   │   ├── node120.members.0.js │   │   ├── node121.members.0.js │   │   ├── node123.members.0.js │   │   ├── node125.members.0.js │   │   ├── node127.members.0.js │   │   ├── node129.members.0.js │   │   ├── node131.members.0.js │   │   ├── node135.members.0.js │   │   ├── node140.members.0.js │   │   ├── node144.members.0.js │   │   ├── node146.members.0.js │   │   ├── node147.members.0.js │   │   ├── node149.members.0.js │   │   ├── node14.members.0.js │   │   ├── node150.members.0.js │   │   ├── node153.members.0.js │   │   ├── node155.members.0.js │   │   ├── node156.members.0.js │   │   ├── node157.members.0.js │   │   ├── node158.members.0.js │   │   ├── node162.members.0.js │   │   ├── node165.members.0.js │   │   ├── node168.members.0.js │   │   ├── node171.members.0.js │   │   ├── node173.members.0.js │   │   ├── node176.members.0.js │   │   ├── node178.members.0.js │   │   ├── node17.members.0.js │   │   ├── node182.members.0.js │   │   ├── node184.members.0.js │   │   ├── node185.members.0.js │   │   ├── node188.members.0.js │   │   ├── node190.members.0.js │   │   ├── node191.members.0.js │   │   ├── node192.members.0.js │   │   ├── node193.members.0.js │   │   ├── node194.members.0.js │   │   ├── node195.members.0.js │   │   ├── node198.members.0.js │   │   ├── node19.members.0.js │   │   ├── node201.members.0.js │   │   ├── node204.members.0.js │   │   ├── node208.members.0.js │   │   ├── node210.members.0.js │   │   ├── node214.members.0.js │   │   ├── node217.members.0.js │   │   ├── node220.members.0.js │   │   ├── node222.members.0.js │   │   ├── node224.members.0.js │   │   ├── node227.members.0.js │   │   ├── node229.members.0.js │   │   ├── node231.members.0.js │   │   ├── node234.members.0.js │   │   ├── node237.members.0.js │   │   ├── node238.members.0.js │   │   ├── node239.members.0.js │   │   ├── node240.members.0.js │   │   ├── node243.members.0.js │   │   ├── node246.members.0.js │   │   ├── node249.members.0.js │   │   ├── node251.members.0.js │   │   ├── node254.members.0.js │   │   ├── node255.members.0.js │   │   ├── node265.members.0.js │   │   ├── node268.members.0.js │   │   ├── node269.members.0.js │   │   ├── node26.members.0.js │   │   ├── node271.members.0.js │   │   ├── node272.members.0.js │   │   ├── node274.members.0.js │   │   ├── node276.members.0.js │   │   ├── node282.members.0.js │   │   ├── node284.members.0.js │   │   ├── node286.members.0.js │   │   ├── node287.members.0.js │   │   ├── node290.members.0.js │   │   ├── node291.members.0.js │   │   ├── node294.members.0.js │   │   ├── node295.members.0.js │   │   ├── node29.members.0.js │   │   ├── node300.members.0.js │   │   ├── node302.members.0.js │   │   ├── node304.members.0.js │   │   ├── node309.members.0.js │   │   ├── node312.members.0.js │   │   ├── node313.members.0.js │   │   ├── node314.members.0.js │   │   ├── node315.members.0.js │   │   ├── node316.members.0.js │   │   ├── node319.members.0.js │   │   ├── node31.members.0.js │   │   ├── node326.members.0.js │   │   ├── node328.members.0.js │   │   ├── node329.members.0.js │   │   ├── node334.members.0.js │   │   ├── node335.members.0.js │   │   ├── node336.members.0.js │   │   ├── node338.members.0.js │   │   ├── node339.members.0.js │   │   ├── node343.members.0.js │   │   ├── node346.members.0.js │   │   ├── node34.members.0.js │   │   ├── node354.members.0.js │   │   ├── node355.members.0.js │   │   ├── node360.members.0.js │   │   ├── node361.members.0.js │   │   ├── node365.members.0.js │   │   ├── node36.members.0.js │   │   ├── node373.members.0.js │   │   ├── node376.members.0.js │   │   ├── node37.members.0.js │   │   ├── node383.members.0.js │   │   ├── node38.members.0.js │   │   ├── node391.members.0.js │   │   ├── node39.members.0.js │   │   ├── node400.members.0.js │   │   ├── node406.members.0.js │   │   ├── node407.members.0.js │   │   ├── node408.members.0.js │   │   ├── node409.members.0.js │   │   ├── node40.members.0.js │   │   ├── node411.members.0.js │   │   ├── node412.members.0.js │   │   ├── node413.members.0.js │   │   ├── node414.members.0.js │   │   ├── node415.members.0.js │   │   ├── node416.members.0.js │   │   ├── node417.members.0.js │   │   ├── node419.members.0.js │   │   ├── node41.members.0.js │   │   ├── node420.members.0.js │   │   ├── node421.members.0.js │   │   ├── node422.members.0.js │   │   ├── node424.members.0.js │   │   ├── node425.members.0.js │   │   ├── node426.members.0.js │   │   ├── node427.members.0.js │   │   ├── node428.members.0.js │   │   ├── node429.members.0.js │   │   ├── node42.members.0.js │   │   ├── node431.members.0.js │   │   ├── node432.members.0.js │   │   ├── node433.members.0.js │   │   ├── node434.members.0.js │   │   ├── node435.members.0.js │   │   ├── node436.members.0.js │   │   ├── node437.members.0.js │   │   ├── node438.members.0.js │   │   ├── node43.members.0.js │   │   ├── node440.members.0.js │   │   ├── node441.members.0.js │   │   ├── node442.members.0.js │   │   ├── node443.members.0.js │   │   ├── node444.members.0.js │   │   ├── node445.members.0.js │   │   ├── node447.members.0.js │   │   ├── node449.members.0.js │   │   ├── node44.members.0.js │   │   ├── node452.members.0.js │   │   ├── node455.members.0.js │   │   ├── node457.members.0.js │   │   ├── node45.members.0.js │   │   ├── node461.members.0.js │   │   ├── node463.members.0.js │   │   ├── node465.members.0.js │   │   ├── node467.members.0.js │   │   ├── node469.members.0.js │   │   ├── node46.members.0.js │   │   ├── node474.members.0.js │   │   ├── node475.members.0.js │   │   ├── node479.members.0.js │   │   ├── node484.members.0.js │   │   ├── node487.members.0.js │   │   ├── node494.members.0.js │   │   ├── node498.members.0.js │   │   ├── node502.members.0.js │   │   ├── node505.members.0.js │   │   ├── node508.members.0.js │   │   ├── node509.members.0.js │   │   ├── node50.members.0.js │   │   ├── node517.members.0.js │   │   ├── node522.members.0.js │   │   ├── node530.members.0.js │   │   ├── node533.members.0.js │   │   ├── node537.members.0.js │   │   ├── node53.members.0.js │   │   ├── node540.members.0.js │   │   ├── node543.members.0.js │   │   ├── node544.members.0.js │   │   ├── node57.members.0.js │   │   ├── node60.members.0.js │   │   ├── node63.members.0.js │   │   ├── node66.members.0.js │   │   ├── node69.members.0.js │   │   ├── node72.members.0.js │   │   ├── node77.members.0.js │   │   ├── node78.members.0.js │   │   ├── node83.members.0.js │   │   ├── node87.members.0.js │   │   ├── node91.members.0.js │   │   ├── node95.members.0.js │   │   ├── node97.members.0.js │   │   └── node99.members.0.js │   ├── krona_stderr │   ├── krona_stdout │   └── krona_tax.lst ├── read-based-taxonomy │   ├── krakViral_class.out_READ │   ├── krakViral.krona.html_READ │   ├── krakViral.krona.html_READ.files │   │   ├── enable.js │   │   ├── node13.members.0.js │   │   ├── node18.members.0.js │   │   ├── node19.members.0.js │   │   ├── node1.members.0.js │   │   ├── node21.members.0.js │   │   ├── node23.members.0.js │   │   ├── node24.members.0.js │   │   ├── node25.members.0.js │   │   ├── node26.members.0.js │   │   ├── node27.members.0.js │   │   ├── node28.members.0.js │   │   ├── node29.members.0.js │   │   ├── node2.members.0.js │   │   ├── node30.members.0.js │   │   ├── node32.members.0.js │   │   ├── node38.members.0.js │   │   ├── node42.members.0.js │   │   ├── node48.members.0.js │   │   ├── node50.members.0.js │   │   ├── node53.members.0.js │   │   ├── node57.members.0.js │   │   ├── node62.members.0.js │   │   ├── node69.members.0.js │   │   ├── node6.members.0.js │   │   ├── node73.members.0.js │   │   └── node78.members.0.js │   ├── krakViral.krona_READ │   ├── krakViral.out_READ │   ├── krakViral_report.out_READ │   ├── krakViral_unclass.out_READ │   ├── reads_kaiju.krona_READ │   ├── reads_kaiju.kron.html_READ │   └── readskaiju.out_READ ├── reads-filtering.log ├── readsNotrRNA_filtered.fq ├── readsNotrRNA_filtered.fq.split │   ├── Forward.fq │   └── Reverse.fq ├── readsToblastn.fasta ├── sample09_not_rRNA.fq ├── sample09_R1_trimmed.fq ├── sample09_R2_trimmed.fq ├── sample09_rRNA.fq ├── sample09_rRNA.log ├── sortmeRNA_wd │   ├── idx -> /remote-storage/DBs/SILVA/idx/ │   ├── kvdb │   │   ├── 000003.log │   │   ├── CURRENT │   │   ├── IDENTITY │   │   ├── LOCK │   │   ├── LOG │   │   ├── MANIFEST-000001 │   │   └── OPTIONS-000005 │   └── readb │   ├── fwd_0.fq │   ├── fwd_10.fq │   ├── fwd_11.fq │   ├── fwd_12.fq │   ├── fwd_13.fq │   ├── fwd_14.fq │   ├── fwd_15.fq │   ├── fwd_1.fq │   ├── fwd_2.fq │   ├── fwd_3.fq │   ├── fwd_4.fq │   ├── fwd_5.fq │   ├── fwd_6.fq │   ├── fwd_7.fq │   ├── fwd_8.fq │   ├── fwd_9.fq │   ├── readfeed │   ├── rev_0.fq │   ├── rev_10.fq │   ├── rev_11.fq │   ├── rev_12.fq │   ├── rev_13.fq │   ├── rev_14.fq │   ├── rev_15.fq │   ├── rev_1.fq │   ├── rev_2.fq │   ├── rev_3.fq │   ├── rev_4.fq │   ├── rev_5.fq │   ├── rev_6.fq │   ├── rev_7.fq │   ├── rev_8.fq │   └── rev_9.fq ├── spades_prokka │   ├── spades_prokka.err │   ├── spades_prokka.faa │   ├── spades_prokka.ffn │   ├── spades_prokka.fna │   ├── spades_prokka.fsa │   ├── spades_prokka.gbk │   ├── spades_prokka.gff │   ├── spades_prokka.log │   ├── spades_prokka.sqn │   ├── spades_prokka.tbl │   ├── spades_prokka.tsv │   └── spades_prokka.txt ├── taxonomy.log ├── trim-galore.log ├── unwanted.txt └── WantedReads.taxonomy.krona.html In following list reports where to find the taxonomic association obtained from each strategy using different DBs: FOLDER [STRATEGY NAME] DB-USED.TAXO-PROGRAM.ASSEMBY-METHOD assembly-based-taxonomy krakViral.krona.html_MEGAHIT reads_kaiju.kron.html_MEGAHIT krakViral.krona.html_SPADES reads_kaiju.kron.html_SPADES clustering-based-taxonomy krakViral.krona.html_OTU reads_kaiju.kron.html_OTU read-based-taxonomy krakViral.krona.html_READ reads_kaiju.kron.html_READ FOLDER [SOURCE FILE - BLASTING] TAXO-PROGRAM assembly-based-MEGAHIT-KRONA-BLAST krona_out.html assembly-based-SPADES-KRONA-BLAST krona_out.html clustering-based-KRONA-BLAST krona_out.html read-based-KRONA-BLAST krona_out.html FOLDER FILE assembly-based/spades_quast icarus.html, report.html assembly-based/megahit_quast icarus.html, report.html assembly-based/megahit_prokka megahit_prokka.gbk, megahit_prokka.gff assembly-based/spades_prokka spades_prokka.gbk, spades_prokka.gff