Generated February 28, 2024
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STEP 12 - Taxonomically assign Bins with "Species Tree" and "GTDB-tk" apps for DBAT-T0 and DBSC-T0 samples and also for all the bins made for the controls of the BONCAT-FACS-MDA procedure to identify all the contaminants that were introduced during these procedures.

Build Species Tree for your Microbial Genomes, optionally including Tree Skeleton of Phylum Exemplars
This app completed without errors in 26m 1s.
Objects
Created Object Name Type Description
DBAT_T-dastool_RAST-annotated_bins_Build-Microbial-SpTree Tree Tree for DBAT-T0 dasTool Bins that did not pair with RefSeq reference genomes when using "Build Microbial SpeciesTree"
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_T-dastool_RAST-annotated_bins_Build-Microbial-SpTree.newick
  • DBAT_T-dastool_RAST-annotated_bins_Build-Microbial-SpTree-labels.newick
  • DBAT_T-dastool_RAST-annotated_bins_Build-Microbial-SpTree.png
  • DBAT_T-dastool_RAST-annotated_bins_Build-Microbial-SpTree.pdf
Build Species Tree for your Microbial Genomes, optionally including Tree Skeleton of Phylum Exemplars
This app completed without errors in 25m 30s.
Objects
Created Object Name Type Description
DBAT_T48-dastool_RAST-annotated_bins_Build-Microbial-SpTree Tree Tree for DBAT-T48 dasTool Bins that did not pair with RefSeq reference genomes when using "Build Microbial SpeciesTree"
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_T48-dastool_RAST-annotated_bins_Build-Microbial-SpTree.newick
  • DBAT_T48-dastool_RAST-annotated_bins_Build-Microbial-SpTree-labels.newick
  • DBAT_T48-dastool_RAST-annotated_bins_Build-Microbial-SpTree.png
  • DBAT_T48-dastool_RAST-annotated_bins_Build-Microbial-SpTree.pdf
Build Species Tree for your Microbial Genomes, optionally including Tree Skeleton of Phylum Exemplars
This app completed without errors in 29m 54s.
Objects
Created Object Name Type Description
DBSC_T0-dastool_RAST-annotated_bins_Build-Microbial-SpTree Tree Tree for DBSC-T0 dasTool Bins that did not pair with RefSeq reference genomes when using "Insert Set of Genomes into SpeciesTree"
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_T0-dastool_RAST-annotated_bins_Build-Microbial-SpTree.newick
  • DBSC_T0-dastool_RAST-annotated_bins_Build-Microbial-SpTree-labels.newick
  • DBSC_T0-dastool_RAST-annotated_bins_Build-Microbial-SpTree.png
  • DBSC_T0-dastool_RAST-annotated_bins_Build-Microbial-SpTree.pdf
Add a user-provided GenomeSet to a KBase SpeciesTree.
This app completed without errors in 5m 32s.
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_T0-dastool_RAST-annotated_bins_SpTree.newick
  • DBAT_T0-dastool_RAST-annotated_bins_SpTree-labels.newick
  • DBAT_T0-dastool_RAST-annotated_bins_SpTree.png
  • DBAT_T0-dastool_RAST-annotated_bins_SpTree.pdf
Add a user-provided GenomeSet to a KBase SpeciesTree.
This app completed without errors in 4m 42s.
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_T48-dastool_RAST-annotated_bins_SpTree.newick
  • DBAT_T48-dastool_RAST-annotated_bins_SpTree-labels.newick
  • DBAT_T48-dastool_RAST-annotated_bins_SpTree.png
  • DBAT_T48-dastool_RAST-annotated_bins_SpTree.pdf
Add a user-provided GenomeSet to a KBase SpeciesTree.
This app completed without errors in 12m 9s.
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_T0-dastool_RAST-annotated_bins_SpTree.newick
  • DBSC_T0-dastool_RAST-annotated_bins_SpTree-labels.newick
  • DBSC_T0-dastool_RAST-annotated_bins_SpTree.png
  • DBSC_T0-dastool_RAST-annotated_bins_SpTree.pdf
Add one or more Genomes to a KBase SpeciesTree.
This app completed without errors in 3m 58s.
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • Controls-only_dastool_RAST-annotated_bin_SpTree.newick
  • Controls-only_dastool_RAST-annotated_bin_SpTree-labels.newick
  • Controls-only_dastool_RAST-annotated_bin_SpTree.png
  • Controls-only_dastool_RAST-annotated_bin_SpTree.pdf
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 39m 12s.
Links
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 1h 18m 43s.
Objects
Created Object Name Type Description
bin.001.fasta_DBAT_T48-dastool_assembly.RAST Genome Taxonomy and taxon_assignment updated with GTDB
bin.002.fasta_DBAT_T48-dastool_assembly.RAST Genome Taxonomy and taxon_assignment updated with GTDB
bin.003.fasta_DBAT_T48-dastool_assembly.RAST Genome Taxonomy and taxon_assignment updated with GTDB
DBAT_T48-dastool_RAST-annotated_bins GenomeSet Taxonomy and taxon_assignment updated with GTDB
Links
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 53m 7s.
Links
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 1h 40m 22s.
Links
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 1h 54m 4s.
Links
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 39m 32s.
Links
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 36m 10s.
Links
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 36m 28s.
Links

STEP 11 - Obtain Assembly objects of MAGs of interest using "Extract Bins as Assemblies from Binned Contigs" and annotate them with RAST to generate "Genome Set" object for DBAT and DBSC MAGs. Since the Controls-only assembly only had a single bin output from DAStool we will also extract the Bins generated with MaxBin2, MetaBAT, and CONCUCT to further assess the taxonomy of contaminating lineages in our samples.

Annotate bacterial or archaeal assemblies and/or assembly sets using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
This app completed without errors in 17m 33s.
Objects
Created Object Name Type Description
bin.003.fasta_DBAT_T0-dastool_assembly.RAST Genome RAST annotation
bin.002.fasta_DBAT_T0-dastool_assembly.RAST Genome RAST annotation
bin.001.fasta_DBAT_T0-dastool_assembly.RAST Genome RAST annotation
bin.005.fasta_DBAT_T0-dastool_assembly.RAST Genome RAST annotation
bin.004.fasta_DBAT_T0-dastool_assembly.RAST Genome RAST annotation
DBAT_T0-dastool_RAST-annotated_bins GenomeSet Genome Set
Summary
Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 707 contigs containing 3016482 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3465 new features were called, of which 36 are non-coding.
Output genome has the following feature types:
	Coding gene                     3429 
	Non-coding repeat                 20 
	Non-coding rna                    16 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.003.fasta_DBAT_T0-dastool_assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 91 contigs containing 1685260 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1754 new features were called, of which 31 are non-coding.
Output genome has the following feature types:
	Coding gene                     1723 
	Non-coding repeat                 17 
	Non-coding rna                    14 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.002.fasta_DBAT_T0-dastool_assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 424 contigs containing 2081359 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2383 new features were called, of which 33 are non-coding.
Output genome has the following feature types:
	Coding gene                     2350 
	Non-coding repeat                  9 
	Non-coding rna                    24 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.001.fasta_DBAT_T0-dastool_assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 933 contigs containing 4493272 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 5238 new features were called, of which 56 are non-coding.
Output genome has the following feature types:
	Coding gene                     5182 
	Non-coding repeat                 24 
	Non-coding rna                    32 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.005.fasta_DBAT_T0-dastool_assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 26 contigs containing 3077230 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2942 new features were called, of which 42 are non-coding.
Output genome has the following feature types:
	Coding gene                     2900 
	Non-coding repeat                  4 
	Non-coding rna                    38 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.004.fasta_DBAT_T0-dastool_assembly succeeded!

Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • annotation_report.DBAT_T0-dastool_RAST-annotated_bins - Microbial Annotation Report
Annotate bacterial or archaeal assemblies and/or assembly sets using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
This app completed without errors in 13m 36s.
Objects
Created Object Name Type Description
bin.001.fasta_DBAT_T48-dastool_assembly.RAST Genome RAST annotation
bin.002.fasta_DBAT_T48-dastool_assembly.RAST Genome RAST annotation
bin.003.fasta_DBAT_T48-dastool_assembly.RAST Genome RAST annotation
DBAT_T48-dastool_RAST-annotated_bins GenomeSet Genome Set
Summary
The RAST algorithm was applied to annotating a genome sequence comprised of 579 contigs containing 5072621 nucleotides. 
No initial gene calls were provided.
Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; selenoproteins; pyrrolysoproteins; repeat regions; crispr.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 5595 new features were called, of which 49 are non-coding.
Output genome has the following feature types:
	Coding gene                     5546 
	Non-coding repeat                 30 
	Non-coding rna                    19 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.001.fasta_DBAT_T48-dastool_assembly succeeded!

The RAST algorithm was applied to annotating a genome sequence comprised of 52 contigs containing 3165680 nucleotides. 
No initial gene calls were provided.
Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; selenoproteins; pyrrolysoproteins; repeat regions; crispr.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3033 new features were called, of which 40 are non-coding.
Output genome has the following feature types:
	Coding gene                     2993 
	Non-coding repeat                  2 
	Non-coding rna                    38 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.002.fasta_DBAT_T48-dastool_assembly succeeded!

The RAST algorithm was applied to annotating a genome sequence comprised of 295 contigs containing 1927562 nucleotides. 
No initial gene calls were provided.
Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; selenoproteins; pyrrolysoproteins; repeat regions; crispr.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2307 new features were called, of which 96 are non-coding.
Output genome has the following feature types:
	Coding gene                     2211 
	Non-coding crispr_array            1 
	Non-coding crispr_repeat          30 
	Non-coding crispr_spacer          29 
	Non-coding repeat                 19 
	Non-coding rna                    17 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.003.fasta_DBAT_T48-dastool_assembly succeeded!

Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • annotation_report.DBAT_T48-dastool_RAST-annotated_bins - Microbial Annotation Report
Annotate bacterial or archaeal assemblies and/or assembly sets using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
This app completed without errors in 2h 7m 40s.
Objects
Created Object Name Type Description
bin.007.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.008.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.005.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.029.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.006.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.028.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.004.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.027.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.025.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.024.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.023.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.050.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.022.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.049.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.003.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.021.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.019.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.048.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.020.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.047.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.046.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.045.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.001.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.018.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.002.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.016.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.017.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.044.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.014.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.042.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.015.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.041.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.012.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.039.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.013.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.037.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.010.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.036.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.011.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.034.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.033.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.009.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.032.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
bin.030.fasta_DBSC_T0-dastool__assembly.RAST Genome RAST annotation
DBSC_T0-dastool_RAST-annotated_bins GenomeSet Genome Set
Summary
Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 424 contigs containing 1513515 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1899 new features were called, of which 30 are non-coding.
Output genome has the following feature types:
	Coding gene                     1869 
	Non-coding repeat                 22 
	Non-coding rna                     8 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.007.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 152 contigs containing 813033 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 913 new features were called, of which 26 are non-coding.
Output genome has the following feature types:
	Coding gene                      887 
	Non-coding rna                    26 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.008.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 64 contigs containing 5923365 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 6103 new features were called, of which 90 are non-coding.
Output genome has the following feature types:
	Coding gene                     6013 
	Non-coding repeat                 46 
	Non-coding rna                    44 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.005.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 210 contigs containing 2822742 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2932 new features were called, of which 40 are non-coding.
Output genome has the following feature types:
	Coding gene                     2892 
	Non-coding repeat                 10 
	Non-coding rna                    30 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.029.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 315 contigs containing 3091155 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3198 new features were called, of which 53 are non-coding.
Output genome has the following feature types:
	Coding gene                     3145 
	Non-coding repeat                 22 
	Non-coding rna                    31 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.006.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 76 contigs containing 3734877 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3755 new features were called, of which 71 are non-coding.
Output genome has the following feature types:
	Coding gene                     3684 
	Non-coding repeat                 28 
	Non-coding rna                    43 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.028.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 255 contigs containing 4497678 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 4527 new features were called, of which 61 are non-coding.
Output genome has the following feature types:
	Coding gene                     4466 
	Non-coding repeat                 24 
	Non-coding rna                    37 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.004.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 166 contigs containing 2396530 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2288 new features were called, of which 42 are non-coding.
Output genome has the following feature types:
	Coding gene                     2246 
	Non-coding repeat                 10 
	Non-coding rna                    32 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.027.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 502 contigs containing 2162247 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2574 new features were called, of which 45 are non-coding.
Output genome has the following feature types:
	Coding gene                     2529 
	Non-coding repeat                  8 
	Non-coding rna                    37 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.025.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 102 contigs containing 3472457 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3384 new features were called, of which 63 are non-coding.
Output genome has the following feature types:
	Coding gene                     3321 
	Non-coding repeat                 16 
	Non-coding rna                    47 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.024.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 14 contigs containing 5699292 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 5294 new features were called, of which 88 are non-coding.
Output genome has the following feature types:
	Coding gene                     5206 
	Non-coding repeat                 37 
	Non-coding rna                    51 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.023.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 246 contigs containing 3883314 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3893 new features were called, of which 44 are non-coding.
Output genome has the following feature types:
	Coding gene                     3849 
	Non-coding repeat                 20 
	Non-coding rna                    24 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.050.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 167 contigs containing 3300905 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3356 new features were called, of which 48 are non-coding.
Output genome has the following feature types:
	Coding gene                     3308 
	Non-coding repeat                  9 
	Non-coding rna                    39 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.022.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 299 contigs containing 2301479 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2560 new features were called, of which 50 are non-coding.
Output genome has the following feature types:
	Coding gene                     2510 
	Non-coding repeat                 16 
	Non-coding rna                    34 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.049.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 621 contigs containing 5090540 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 5062 new features were called, of which 43 are non-coding.
Output genome has the following feature types:
	Coding gene                     5019 
	Non-coding repeat                  8 
	Non-coding rna                    35 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.003.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 79 contigs containing 3066097 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2695 new features were called, of which 47 are non-coding.
Output genome has the following feature types:
	Coding gene                     2648 
	Non-coding repeat                  8 
	Non-coding rna                    39 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.021.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 376 contigs containing 2268695 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2157 new features were called, of which 15 are non-coding.
Output genome has the following feature types:
	Coding gene                     2142 
	Non-coding rna                    15 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.019.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 692 contigs containing 3867563 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 4128 new features were called, of which 31 are non-coding.
Output genome has the following feature types:
	Coding gene                     4097 
	Non-coding repeat                  6 
	Non-coding rna                    25 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.048.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 204 contigs containing 2429254 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2382 new features were called, of which 21 are non-coding.
Output genome has the following feature types:
	Coding gene                     2361 
	Non-coding rna                    21 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.020.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 123 contigs containing 2814484 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2849 new features were called, of which 35 are non-coding.
Output genome has the following feature types:
	Coding gene                     2814 
	Non-coding repeat                 10 
	Non-coding rna                    25 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.047.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 232 contigs containing 2364156 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2589 new features were called, of which 16 are non-coding.
Output genome has the following feature types:
	Coding gene                     2573 
	Non-coding repeat                  2 
	Non-coding rna                    14 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.046.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 191 contigs containing 3817923 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3946 new features were called, of which 49 are non-coding.
Output genome has the following feature types:
	Coding gene                     3897 
	Non-coding repeat                 23 
	Non-coding rna                    26 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.045.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 331 contigs containing 2008399 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1946 new features were called, of which 45 are non-coding.
Output genome has the following feature types:
	Coding gene                     1901 
	Non-coding repeat                  8 
	Non-coding rna                    37 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.001.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 66 contigs containing 1153613 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1059 new features were called, of which 37 are non-coding.
Output genome has the following feature types:
	Coding gene                     1022 
	Non-coding rna                    37 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.018.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 406 contigs containing 1905671 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2070 new features were called, of which 29 are non-coding.
Output genome has the following feature types:
	Coding gene                     2041 
	Non-coding repeat                 18 
	Non-coding rna                    11 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.002.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 207 contigs containing 3505820 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3501 new features were called, of which 34 are non-coding.
Output genome has the following feature types:
	Coding gene                     3467 
	Non-coding repeat                  9 
	Non-coding rna                    25 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.016.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 198 contigs containing 1225435 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1320 new features were called, of which 16 are non-coding.
Output genome has the following feature types:
	Coding gene                     1304 
	Non-coding rna                    16 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.017.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 441 contigs containing 5053084 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 5198 new features were called, of which 55 are non-coding.
Output genome has the following feature types:
	Coding gene                     5143 
	Non-coding repeat                 20 
	Non-coding rna                    35 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.044.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 268 contigs containing 2178708 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2403 new features were called, of which 87 are non-coding.
Output genome has the following feature types:
	Coding gene                     2316 
	Non-coding repeat                 56 
	Non-coding rna                    31 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.014.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 75 contigs containing 3897872 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3821 new features were called, of which 53 are non-coding.
Output genome has the following feature types:
	Coding gene                     3768 
	Non-coding repeat                  8 
	Non-coding rna                    45 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.042.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 162 contigs containing 1149879 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1193 new features were called, of which 34 are non-coding.
Output genome has the following feature types:
	Coding gene                     1159 
	Non-coding repeat                  2 
	Non-coding rna                    32 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.015.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 344 contigs containing 1813786 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2217 new features were called, of which 62 are non-coding.
Output genome has the following feature types:
	Coding gene                     2155 
	Non-coding repeat                 12 
	Non-coding rna                    50 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.041.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 65 contigs containing 1507293 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1387 new features were called, of which 41 are non-coding.
Output genome has the following feature types:
	Coding gene                     1346 
	Non-coding rna                    41 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.012.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 144 contigs containing 1834473 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1674 new features were called, of which 44 are non-coding.
Output genome has the following feature types:
	Coding gene                     1630 
	Non-coding repeat                 12 
	Non-coding rna                    32 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.039.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 222 contigs containing 6248263 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 6243 new features were called, of which 104 are non-coding.
Output genome has the following feature types:
	Coding gene                     6139 
	Non-coding repeat                 57 
	Non-coding rna                    47 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.013.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 118 contigs containing 8006443 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 7927 new features were called, of which 73 are non-coding.
Output genome has the following feature types:
	Coding gene                     7854 
	Non-coding repeat                 39 
	Non-coding rna                    34 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.037.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 19 contigs containing 2976895 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2842 new features were called, of which 40 are non-coding.
Output genome has the following feature types:
	Coding gene                     2802 
	Non-coding repeat                  2 
	Non-coding rna                    38 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.010.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 123 contigs containing 1413280 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1452 new features were called, of which 40 are non-coding.
Output genome has the following feature types:
	Coding gene                     1412 
	Non-coding repeat                 10 
	Non-coding rna                    30 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.036.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 101 contigs containing 1658799 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1649 new features were called, of which 28 are non-coding.
Output genome has the following feature types:
	Coding gene                     1621 
	Non-coding rna                    28 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.011.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 238 contigs containing 1334195 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 1470 new features were called, of which 20 are non-coding.
Output genome has the following feature types:
	Coding gene                     1450 
	Non-coding repeat                  6 
	Non-coding rna                    14 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.034.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 569 contigs containing 2785019 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 3069 new features were called, of which 28 are non-coding.
Output genome has the following feature types:
	Coding gene                     3041 
	Non-coding repeat                 18 
	Non-coding rna                    10 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.033.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 100 contigs containing 4828815 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 4851 new features were called, of which 106 are non-coding.
Output genome has the following feature types:
	Coding gene                     4745 
	Non-coding repeat                 61 
	Non-coding rna                    45 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.009.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 637 contigs containing 4942726 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 4713 new features were called, of which 106 are non-coding.
Output genome has the following feature types:
	Coding gene                     4607 
	Non-coding repeat                 72 
	Non-coding rna                    34 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.032.fasta_DBSC_T0-dastool__assembly succeeded!

Some RAST tools will not run unless the taxonomic domain is Archaea, Bacteria, or Virus. 
These tools include: call selenoproteins, call pyrroysoproteins, call crisprs, and call prophage phispy features.
You may not get the results you were expecting with your current domain of U.
The RAST algorithm was applied to annotating a genome sequence comprised of 501 contigs containing 4667328 nucleotides. 
No initial gene calls were provided.
Did not call selenoproteins because the domain is U

Did not call pyrrolysoproteins because the domain is U

Did not call crisprs because the domain is U

Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; repeat regions.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 4352 new features were called, of which 79 are non-coding.
Output genome has the following feature types:
	Coding gene                     4273 
	Non-coding repeat                 41 
	Non-coding rna                    38 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
bin.030.fasta_DBSC_T0-dastool__assembly succeeded!

Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • annotation_report.DBSC_T0-dastool_RAST-annotated_bins - Microbial Annotation Report
Annotate a bacterial or archaeal assembly using RASTtk (Rapid Annotations using Subsystems Technology toolkit).
This app completed without errors in 3m 18s.
Objects
Created Object Name Type Description
Controls-only_dastool_bin_genome Genome RAST annotation
Summary
The RAST algorithm was applied to annotating a genome sequence comprised of 22 contigs containing 3028300 nucleotides. 
No initial gene calls were provided.
Standard features were called using: glimmer3; prodigal.
A scan was conducted for the following additional feature types: rRNA; tRNA; selenoproteins; pyrrolysoproteins; repeat regions; crispr.
The genome features were functionally annotated using the following algorithm(s): Kmers V2; Kmers V1; protein similarity.
In addition to the remaining original 0 coding features and 0 non-coding features, 2892 new features were called, of which 37 are non-coding.
Output genome has the following feature types:
	Coding gene                     2855 
	Non-coding repeat                  2 
	Non-coding rna                    35 
Overall, the genes have 0 distinct functions. 
The genes include 0 genes with a SEED annotation ontology across 0 distinct SEED functions.
The number of distinct functions can exceed the number of genes because some genes have multiple functions.
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 2m 59s.
Objects
Created Object Name Type Description
_DBAT_T0-dastool_extracted_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
bin.001.fasta_DBAT_T0-dastool_assembly Assembly Assembly object of extracted contigs
bin.002.fasta_DBAT_T0-dastool_assembly Assembly Assembly object of extracted contigs
bin.003.fasta_DBAT_T0-dastool_assembly Assembly Assembly object of extracted contigs
bin.004.fasta_DBAT_T0-dastool_assembly Assembly Assembly object of extracted contigs
bin.005.fasta_DBAT_T0-dastool_assembly Assembly Assembly object of extracted contigs
Summary
Job Finished Generated Assembly Reference: 90888/905/1, 90888/906/1, 90888/908/1, 90888/910/1, 90888/912/1 Generated Assembly Set: 90888/913/1
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 2m 1s.
Objects
Created Object Name Type Description
_DBAT_T48-dastool_extracted_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
bin.003.fasta_DBAT_T48-dastool_assembly Assembly Assembly object of extracted contigs
bin.002.fasta_DBAT_T48-dastool_assembly Assembly Assembly object of extracted contigs
bin.001.fasta_DBAT_T48-dastool_assembly Assembly Assembly object of extracted contigs
Summary
Job Finished Generated Assembly Reference: 90888/1012/1, 90888/1013/1, 90888/1014/1 Generated Assembly Set: 90888/1015/1
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 19m 57s.
Objects
Created Object Name Type Description
_DBSC_T0-dastool_extracted_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
bin.001.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.002.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.003.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.004.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.005.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.006.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.007.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.008.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.009.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.010.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.011.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.012.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.013.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.014.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.015.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.016.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.017.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.018.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.019.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.020.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.021.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.022.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.023.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.024.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.025.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.027.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.028.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.029.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.030.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.032.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.033.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.034.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.036.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.037.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.039.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.041.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.042.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.044.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.045.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.046.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.047.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.048.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.049.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
bin.050.fasta_DBSC_T0-dastool__assembly Assembly Assembly object of extracted contigs
Summary
Job Finished Generated Assembly Reference: 90888/907/1, 90888/909/1, 90888/911/1, 90888/914/1, 90888/916/1, 90888/917/1, 90888/918/1, 90888/919/1, 90888/920/1, 90888/921/1, 90888/922/1, 90888/923/1, 90888/924/1, 90888/925/1, 90888/926/1, 90888/927/1, 90888/928/1, 90888/929/1, 90888/930/1, 90888/931/1, 90888/932/1, 90888/933/1, 90888/934/1, 90888/935/1, 90888/936/1, 90888/937/1, 90888/938/1, 90888/939/1, 90888/940/1, 90888/941/1, 90888/942/1, 90888/943/1, 90888/944/1, 90888/945/1, 90888/946/1, 90888/947/1, 90888/948/1, 90888/949/1, 90888/950/1, 90888/951/1, 90888/952/1, 90888/953/1, 90888/954/1, 90888/955/1 Generated Assembly Set: 90888/956/1
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 1m 10s.
Objects
Created Object Name Type Description
bin.001.fastaControls-only_dastool_bin_assembly Assembly Assembly object of extracted contigs
Summary
Job Finished Generated Assembly Reference: 90888/993/1
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 6m 9s.
Objects
Created Object Name Type Description
_Controls-contaminats_CONCUCT_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
bin.005.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.012.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.003.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.009.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.011.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.000.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.001.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.010.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.004.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.008.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.002.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.007.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
bin.006.fasta_Controls-contaminats_CONCUCT_assembly Assembly Assembly object of extracted contigs
Summary
Job Finished Generated Assembly Reference: 90888/1082/1, 90888/1085/1, 90888/1089/1, 90888/1095/1, 90888/1096/1, 90888/1097/1, 90888/1098/1, 90888/1099/1, 90888/1100/1, 90888/1101/1, 90888/1102/1, 90888/1103/1, 90888/1104/1 Generated Assembly Set: 90888/1105/1
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 58s.
Objects
Created Object Name Type Description
bin.001.fasta_Controls-contaminats_MetaBAT2_assembly Assembly Assembly object of extracted contigs
Summary
Job Finished Generated Assembly Reference: 90888/1083/1
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 1m 28s.
Objects
Created Object Name Type Description
_Controls-contaminats_Maxbin2_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
Bin.001.fasta_Controls-contaminats_Maxbin2_assembly Assembly Assembly object of extracted contigs
Bin.002.fasta_Controls-contaminats_Maxbin2_assembly Assembly Assembly object of extracted contigs
Summary
Job Finished Generated Assembly Reference: 90888/1087/1, 90888/1090/1 Generated Assembly Set: 90888/1092/1
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 1m 28s.
Objects
Created Object Name Type Description
_Controls-contaminats_Maxbin2_40_bins.AssemblySet AssemblySet Assembly set of extracted assemblies
Bin.002.fasta_Controls-contaminats_Maxbin2_40_assembly Assembly Assembly object of extracted contigs
Bin.001.fasta_Controls-contaminats_Maxbin2_40_assembly Assembly Assembly object of extracted contigs
Summary
Job Finished Generated Assembly Reference: 90888/1086/1, 90888/1088/1 Generated Assembly Set: 90888/1091/1

STEP 10 - Bin MAG quality control and extraction

Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
This app completed without errors in 9m 52s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
This app completed without errors in 7m 36s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
This app completed without errors in 48m 24s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
This app completed without errors in 5m 46s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM

STEP 009 - Bin MAGs from assembled T0 metagenomes (those from the same sampling site co-assembly), and each T0 and T48 metagenome separately:

  • Atacama Trench:

T0 communities = Niskin 12L T0 whole sample (DBAT_01), PRS T0 whole sample (DBAT_02), Niskin 12L T0 sort of all cells (DBAT_11), PRS T0 sort of all cells (DBAT_12), PRS T0 sort of BONCAT+ cells (DBAT_13).

  • San Clemente metagenomes:

T0 communities = Niskin 30L T0 0.2-3um (DBSC_07), Niskin 30L T0 3-20um (DBSC_08), Niskin 3.5L T0 0.2-3um (DBSC_10), Niskin 3.5L T0 3-20um (DBSC_11), PRS T0 whole sample (DBSC_12), and Niskin 30L T0 whole sample (DBSC_31).

  • Each T48 metagenome was also binned using its individual assembly whenever the metagenomic reads passed the Trimmomatic quality filtration

1- MaxBin2 (https://narrative.kbase.us/#catalog/apps/kb_maxbin/run_maxbin2/release) using 107 Bacterial marker genes

2- MaxBin2 (https://narrative.kbase.us/#catalog/apps/kb_maxbin/run_maxbin2/release) using 40 Archaeal and Bacterial marker genes

3- MetaBAT2 (https://narrative.kbase.us/#catalog/apps/metabat/run_metabat/release)

4- CONCOCT (https://narrative.kbase.us/#catalog/apps/kb_concoct/run_kb_concoct/release)

5- Then all the bins were further refined using the DAS Tool app to obtain a final Binning output for each metagenome of interest.

STEP 009-5 Refine all the T0 co-assemblies and all the T48 individual sample assemblies with DAStool

Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
This app completed without errors in 2m 17s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • das_tool_result.zip - Files generated by kb_das_tool App
Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
This app completed without errors in 4m 3s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • das_tool_result.zip - Files generated by kb_das_tool App
Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
This app completed without errors in 3m 17s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • das_tool_result.zip - Files generated by kb_das_tool App
Optimize bacterial or archaeal genome bins using a dereplication, aggregation and scoring strategy
This app completed without errors in 24m 35s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • das_tool_result.zip - Files generated by kb_das_tool App

STEP 009-4 Run CONCOCT on T0 co-assemblies and on all T48 individual sample assemblies using default parameters

Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
This app completed without errors in 2h 49m 24s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • concoct_result.zip - Files generated by CONCOCT App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
This app completed without errors in 1h 23m 6s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • concoct_result.zip - Files generated by CONCOCT App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
This app completed without errors in 1h 55m 1s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • concoct_result.zip - Files generated by CONCOCT App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage and nucleotide composition
This app completed without errors in 23m 3s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • concoct_result.zip - Files generated by CONCOCT App

STEP 009-3 Run MetaBAT2 on T0 co-assemblies and on all T48 individual sample assemblies using default parameters

Bin metagenomic contigs
This app completed without errors in 2h 4m 52s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • metabat_result.zip - Files generated by MetaBAT2 App
Bin metagenomic contigs
This app completed without errors in 49m 52s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • metabat_result.zip - Files generated by MetaBAT2 App
Bin metagenomic contigs
This app completed without errors in 1h 9m 34s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • metabat_result.zip - Files generated by MetaBAT2 App
Bin metagenomic contigs
This app completed without errors in 14m 44s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • metabat_result.zip - Files generated by MetaBAT2 App

STEP 009-2 Run MaxBin2 on T0 co-assemblies using the 40 Archaeal & Bacterial marker genes setting.

Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 59m 8s.
Objects
Created Object Name Type Description
DBAT_all-T48_SPAdes_MAXbin2_40binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 4h 13m 44s.
Objects
Created Object Name Type Description
DBSC_all-T0_SPAdes_MAXbin2_40binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 1h 9m 58s.
Objects
Created Object Name Type Description
DBAT_all-T0_SPAdes_MAXbin2_40binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 14m 6s.
Objects
Created Object Name Type Description
Controls_contaminants_SPAdes_MAXbin2_40binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App

STEP 009-1 Run MaxBin2 on T0 co-assemblies using the 107 Bacterial marker genes setting.

Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 1h 14m 39s.
Objects
Created Object Name Type Description
DBAT_all-T0_SPAdes_MAXbin2_binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 1h 16m 26s.
Objects
Created Object Name Type Description
DBAT_all-T0_SPAdes_MAXbin2_3kbp-binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 1h 17m 34s.
Objects
Created Object Name Type Description
DBAT_all-T0_SPAdes_MAXbin2_2.5kbp-binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 1h 0m 55s.
Objects
Created Object Name Type Description
DBAT_all-T48_SPAdes_MAXbin2_binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 4h 3m 4s.
Objects
Created Object Name Type Description
DBSC_all-T0_SPAdes_MAXbin2_binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 3h 33m 59s.
Objects
Created Object Name Type Description
DBSC_all-T0_SPAdes_MAXbin2_2.5kbp-binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 3h 5m 16s.
Objects
Created Object Name Type Description
DBSC_all-T0_SPAdes_MAXbin2_3.0kbp-binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Group assembled metagenomic contigs into lineages (Bins) using depth-of-coverage, nucleotide composition, and marker genes.
This app completed without errors in 14m 10s.
Objects
Created Object Name Type Description
Controls_contaminants_SPAdes_MAXbin2_binns BinnedContigs BinnedContigs from MaxBin2
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • maxbin_result.zip - File(s) generated by MaxBin2 App

STEP 008 - Preliminary taxonomic assignation of unassembled quality-filtered read sets from the same experiments using Kaiju app:

1- Atacama Trench Niskin vs PRS vs NegCtrl

2- Sn Clemente MDAs from Niskin, PRS, and negative controls, as well as 48h incubations at 0.1MPa and 20MPa.

Allows users to perform taxonomic classification of shotgun metagenomic read data with Kaiju.
This app completed without errors in 10h 33m 55s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • kaiju_classifications.zip
  • kaiju_summaries.zip
  • krona_data.zip
  • stacked_bar_abundance_plots_PNG+PDF.zip
Allows users to perform taxonomic classification of shotgun metagenomic read data with Kaiju.
This app completed without errors in 5h 34m 38s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • kaiju_classifications.zip
  • kaiju_summaries.zip
  • krona_data.zip
  • stacked_bar_abundance_plots_PNG+PDF.zip
Allows users to perform taxonomic classification of shotgun metagenomic read data with Kaiju.
This app completed without errors in 18h 41m 18s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • kaiju_classifications.zip
  • kaiju_summaries.zip
  • krona_data.zip
  • stacked_bar_abundance_plots_PNG+PDF.zip

STEP 007 - Merge Reads Libraries and co-assemble all samples retrieved simultaneously (same cast / deployment and depth, but collected with Niskin bottles or PRSs) and processed 0h after retrieval or 48h of incubation from:

A) 7000m in the Atacama Trench

B) 2000m in the San Clemente Basin

C) Also, Merge Reads Libraries and co-assemble all Control samples from the BONCAT-FACS-MDA process to identify the contaminant microbes, make MAGs for the most prominent representatives and remove these "contaminant-related" data from downstream analysis.

... These co-assemblies will provide deeper seqeuncing to this water parcels and allow for the generation of MAGs (see "STEP 009").

Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 6h 24m 27s.
Objects
Created Object Name Type Description
Controls-CONTAM_metaSPAdes.Assembly_2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/Controls-CONTAM_metaSPAdes.Assembly_2Kcontigs Assembled into 1054 contigs. Avg Length: 7302.413662239089 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 1042 -- 2001.0 to 88614.1 bp 6 -- 88614.1 to 175227.2 bp 4 -- 175227.2 to 261840.30000000002 bp 1 -- 261840.30000000002 to 348453.4 bp 0 -- 348453.4 to 435066.5 bp 0 -- 435066.5 to 521679.60000000003 bp 0 -- 521679.60000000003 to 608292.7000000001 bp 0 -- 608292.7000000001 to 694905.8 bp 0 -- 694905.8 to 781518.9 bp 1 -- 781518.9 to 868132.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1d 8h 10m 52s.
Objects
Created Object Name Type Description
AtacamaTrench_T48_metaSPAdes.Assembly_2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/AtacamaTrench_T48_metaSPAdes.Assembly_2Kcontigs Assembled into 3007 contigs. Avg Length: 7433.171267043565 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 2996 -- 2002.0 to 88615.0 bp 5 -- 88615.0 to 175228.0 bp 3 -- 175228.0 to 261841.0 bp 2 -- 261841.0 to 348454.0 bp 0 -- 348454.0 to 435067.0 bp 0 -- 435067.0 to 521680.0 bp 0 -- 521680.0 to 608293.0 bp 0 -- 608293.0 to 694906.0 bp 0 -- 694906.0 to 781519.0 bp 1 -- 781519.0 to 868132.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 23h 8m 26s.
Objects
Created Object Name Type Description
AtacamaTrench_T0_metaSPAdes.Assembly_2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/AtacamaTrench_T0_metaSPAdes.Assembly_2Kcontigs Assembled into 5267 contigs. Avg Length: 6882.784887032466 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 5210 -- 2000.0 to 45451.2 bp 33 -- 45451.2 to 88902.4 bp 9 -- 88902.4 to 132353.59999999998 bp 5 -- 132353.59999999998 to 175804.8 bp 3 -- 175804.8 to 219256.0 bp 4 -- 219256.0 to 262707.19999999995 bp 1 -- 262707.19999999995 to 306158.39999999997 bp 0 -- 306158.39999999997 to 349609.6 bp 1 -- 349609.6 to 393060.8 bp 1 -- 393060.8 to 436512.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1d 16h 39m 45s.
Objects
Created Object Name Type Description
SanClemente_T0_metaSPAdes.Assembly_2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/SanClemente_T0_metaSPAdes.Assembly_2Kcontigs Assembled into 71698 contigs. Avg Length: 5779.740369326899 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 71601 -- 2000.0 to 130082.7 bp 72 -- 130082.7 to 258165.4 bp 14 -- 258165.4 to 386248.1 bp 5 -- 386248.1 to 514330.8 bp 3 -- 514330.8 to 642413.5 bp 0 -- 642413.5 to 770496.2 bp 0 -- 770496.2 to 898578.9 bp 1 -- 898578.9 to 1026661.6 bp 1 -- 1026661.6 to 1154744.3 bp 1 -- 1154744.3 to 1282827.0 bp
Links
Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
This app completed without errors in 15m 31s.
Objects
Created Object Name Type Description
Controls_BONCAT-FACS-MDA_all_contaminants PairedEndLibrary BONCAT-FACS-MDA negative controls representing handling-related contaminants of this processing
Summary
NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 2
Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
This app completed without errors in 53m 23s.
Objects
Created Object Name Type Description
Atacama_Trench_all_T48_metaGs_plus_Crls PairedEndLibrary Atacama Trench 7000m all metagenome samples incubated for 48h after retrieval (in PRS) at 4oC and in situ pressure, plus negative controls to identify MDA contaminant sequences
Summary
NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 5
Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
This app completed without errors in 1h 6m 13s.
Objects
Created Object Name Type Description
San_Clemente_T48_BONCATpositive_metaGs_plus_Ctrls PairedEndLibrary San Clemente basin 2000m metagenomes of samples all "BONCAT+" incubated 48h after retrieval (Niskins and PRS) plus MDA controls
Summary
NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 6
Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
This app completed without errors in 1h 26m 50s.
Objects
Created Object Name Type Description
San_Clemente_T0_all_metaGs_plus_Ctrls PairedEndLibrary San Clemente basin 2000m metagenomes of samples processed 0h after retrieval (Niskins and PRS) plus MDA controls
Summary
NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 7
Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
This app completed without errors in 59m 27s.
Objects
Created Object Name Type Description
Atacama_Trench_all_T0_metaGs_plus_Ctrls PairedEndLibrary Atacama Trench 7000m all metagenome samples processed 0h after retrieval (Niskin and PRS) plus negative controls to identify MDA contaminant sequences
Summary
NUM READS LIBRARIES COMBINED INTO ONE READS LIBRARY: 7

STEP 006 - Build Reads Sets of comparable samples for a preliminary taxonomic composition comparison (see "STEP 008")

Allows users to create a ReadsSet object.
This app completed without errors in 10s.
Objects
Created Object Name Type Description
-SC-_DBSC_07-31_and_SORT-ctrls ReadsSet KButil_Build_ReadsSet
Summary
reads libs in output set -SC-_DBSC_07-31_and_SORT-ctrls: 21
Allows users to create a ReadsSet object.
This app completed without errors in 9s.
Objects
Created Object Name Type Description
-AT-_all_DBAT_read_libraries_01-05_11-13_and_SORT-ctrls ReadsSet KButil_Build_ReadsSet
Summary
reads libs in output set -AT-_all_DBAT_read_libraries_01-05_11-13_and_SORT-ctrls: 10
Allows users to create a ReadsSet object.
This app completed without errors in 12s.
Objects
Created Object Name Type Description
-AT-_natural_DBAT_read_libraries_01-05_no-enrichments_no-SORT_no-ctrls ReadsSet KButil_Build_ReadsSet
Summary
reads libs in output set -AT-_natural_DBAT_read_libraries_01-05_no-enrichments_no-SORT_no-ctrls: 4

STEP 005 - Compare San Clemente PRS sample (DBSC_12) with those taken simoultaneously with a 30L Niskin bottle (DBSC_07 and DBSC_31) to see if the few contigs obtained are short or long. Notably, DBSC_12 (11,724,740 reads) and DBSC_31 (12,643,044 reads) have similar number of quality filtered reads but the latter assembled much more long contigs (>2Kbp) then the former.

View distributions of contig characteristics for different assemblies.
This app completed without errors in 3m 6s.
Summary
ASSEMBLY STATS for DBSC_07_SPAdes.2Kcontigs Len longest contig: 1452766 bp N50 (L50): 6998 (4231) N75 (L75): 3323 (13002) N90 (L90): 2403 (21638) Num contigs >= 1000000 bp: 2 Num contigs >= 100000 bp: 58 Num contigs >= 10000 bp: 2533 Num contigs >= 1000 bp: 28996 Num contigs >= 500 bp: 28996 Num contigs >= 1 bp: 28996 Len contigs >= 1000000 bp: 2464954 bp Len contigs >= 100000 bp: 15328911 bp Len contigs >= 10000 bp: 66442675 bp Len contigs >= 1000 bp: 160827968 bp Len contigs >= 500 bp: 160827968 bp Len contigs >= 1 bp: 160827968 bp ASSEMBLY STATS for DBSC_12_SPAdes.2Kcontigs Len longest contig: 245753 bp N50 (L50): 35460 (95) N75 (L75): 11909 (227) N90 (L90): 4815 (442) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 8 Num contigs >= 10000 bp: 267 Num contigs >= 1000 bp: 805 Num contigs >= 500 bp: 805 Num contigs >= 1 bp: 805 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 1115789 bp Len contigs >= 10000 bp: 8836267 bp Len contigs >= 1000 bp: 11198477 bp Len contigs >= 500 bp: 11198477 bp Len contigs >= 1 bp: 11198477 bp ASSEMBLY STATS for DBSC_31_metaSPAdes.Assembly.2Kcontigs Len longest contig: 1320154 bp N50 (L50): 24985 (694) N75 (L75): 6610 (2831) N90 (L90): 3008 (6371) Num contigs >= 1000000 bp: 1 Num contigs >= 100000 bp: 121 Num contigs >= 10000 bp: 1849 Num contigs >= 1000 bp: 10596 Num contigs >= 500 bp: 10596 Num contigs >= 1 bp: 10596 Len contigs >= 1000000 bp: 1320154 bp Len contigs >= 100000 bp: 24849035 bp Len contigs >= 10000 bp: 68564514 bp Len contigs >= 1000 bp: 101947175 bp Len contigs >= 500 bp: 101947175 bp Len contigs >= 1 bp: 101947175 bp
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • key_plot.png
  • key_plot.pdf
  • cumulative_len_plot.png
  • cumulative_len_plot.pdf
  • sorted_contig_lengths.png
  • sorted_contig_lengths.pdf
  • histogram_figures.zip

STEP 004 - Assemble each metagenome separately with metaSPAdes using the quality filtered reads and keeping only contigs of >2Kbp

Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 12h 41m 42s.
Objects
Created Object Name Type Description
DB_SORT_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DB_SORT_SPAdes.2Kcontigs Assembled into 1022 contigs. Avg Length: 4571.353228962818 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 780 -- 2001.0 to 5391.8 bp 158 -- 5391.8 to 8782.6 bp 50 -- 8782.6 to 12173.400000000001 bp 14 -- 12173.400000000001 to 15564.2 bp 8 -- 15564.2 to 18955.0 bp 7 -- 18955.0 to 22345.800000000003 bp 4 -- 22345.800000000003 to 25736.600000000002 bp 0 -- 25736.600000000002 to 29127.4 bp 0 -- 29127.4 to 32518.2 bp 1 -- 32518.2 to 35909.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 7h 25m 29s.
Objects
Created Object Name Type Description
DBSC_31_metaSPAdes.Assembly.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_31_metaSPAdes.Assembly.2Kcontigs Assembled into 10596 contigs. Avg Length: 9621.288693846735 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 10518 -- 2000.0 to 133815.4 bp 55 -- 133815.4 to 265630.8 bp 14 -- 265630.8 to 397446.19999999995 bp 6 -- 397446.19999999995 to 529261.6 bp 0 -- 529261.6 to 661077.0 bp 1 -- 661077.0 to 792892.3999999999 bp 0 -- 792892.3999999999 to 924707.7999999999 bp 1 -- 924707.7999999999 to 1056523.2 bp 0 -- 1056523.2 to 1188338.5999999999 bp 1 -- 1188338.5999999999 to 1320154.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 2h 22m 58s.
Objects
Created Object Name Type Description
DBSC_30_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_30_SPAdes.2Kcontigs Assembled into 585 contigs. Avg Length: 18108.011965811966 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 504 -- 2006.0 to 32299.9 bp 44 -- 32299.9 to 62593.8 bp 19 -- 62593.8 to 92887.70000000001 bp 7 -- 92887.70000000001 to 123181.6 bp 3 -- 123181.6 to 153475.5 bp 3 -- 153475.5 to 183769.40000000002 bp 0 -- 183769.40000000002 to 214063.30000000002 bp 2 -- 214063.30000000002 to 244357.2 bp 2 -- 244357.2 to 274651.10000000003 bp 1 -- 274651.10000000003 to 304945.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 18h 12m 21s.
Objects
Created Object Name Type Description
DBSC_28_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_28_SPAdes.2Kcontigs Assembled into 1668 contigs. Avg Length: 8424.25 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 1452 -- 2004.0 to 16240.6 bp 155 -- 16240.6 to 30477.2 bp 36 -- 30477.2 to 44713.8 bp 15 -- 44713.8 to 58950.4 bp 5 -- 58950.4 to 73187.0 bp 4 -- 73187.0 to 87423.6 bp 0 -- 87423.6 to 101660.2 bp 0 -- 101660.2 to 115896.8 bp 0 -- 115896.8 to 130133.40000000001 bp 1 -- 130133.40000000001 to 144370.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 20h 56m 14s.
Objects
Created Object Name Type Description
DBSC_27_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_27_SPAdes.2Kcontigs Assembled into 424 contigs. Avg Length: 5598.823113207547 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 362 -- 2000.0 to 8338.7 bp 35 -- 8338.7 to 14677.4 bp 12 -- 14677.4 to 21016.1 bp 9 -- 21016.1 to 27354.8 bp 3 -- 27354.8 to 33693.5 bp 2 -- 33693.5 to 40032.2 bp 0 -- 40032.2 to 46370.9 bp 0 -- 46370.9 to 52709.6 bp 0 -- 52709.6 to 59048.299999999996 bp 1 -- 59048.299999999996 to 65387.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 7h 58m 29s.
Objects
Created Object Name Type Description
DBSC_26_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_26_SPAdes.2Kcontigs Assembled into 2018 contigs. Avg Length: 9168.170961347869 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 1494 -- 2000.0 to 11103.6 bp 287 -- 11103.6 to 20207.2 bp 145 -- 20207.2 to 29310.800000000003 bp 59 -- 29310.800000000003 to 38414.4 bp 18 -- 38414.4 to 47518.0 bp 6 -- 47518.0 to 56621.600000000006 bp 3 -- 56621.600000000006 to 65725.20000000001 bp 3 -- 65725.20000000001 to 74828.8 bp 2 -- 74828.8 to 83932.40000000001 bp 1 -- 83932.40000000001 to 93036.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 12h 55m 58s.
Objects
Created Object Name Type Description
DBSC_25_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_25_SPAdes.2Kcontigs Assembled into 1717 contigs. Avg Length: 3593.3727431566685 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 1479 -- 1000.0 to 6700.7 bp 160 -- 6700.7 to 12401.4 bp 48 -- 12401.4 to 18102.1 bp 17 -- 18102.1 to 23802.8 bp 8 -- 23802.8 to 29503.5 bp 2 -- 29503.5 to 35204.2 bp 2 -- 35204.2 to 40904.9 bp 0 -- 40904.9 to 46605.6 bp 0 -- 46605.6 to 52306.299999999996 bp 1 -- 52306.299999999996 to 58007.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 11h 47m 57s.
Objects
Created Object Name Type Description
DBSC_24_SPAdes.2kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_24_SPAdes.2kcontigs Assembled into 715 contigs. Avg Length: 7435.9384615384615 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 565 -- 2003.0 to 9522.3 bp 88 -- 9522.3 to 17041.6 bp 30 -- 17041.6 to 24560.9 bp 17 -- 24560.9 to 32080.2 bp 5 -- 32080.2 to 39599.5 bp 4 -- 39599.5 to 47118.8 bp 1 -- 47118.8 to 54638.1 bp 3 -- 54638.1 to 62157.4 bp 0 -- 62157.4 to 69676.7 bp 2 -- 69676.7 to 77196.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 6h 16m 12s.
Objects
Created Object Name Type Description
DBSC_23_SPAdes.2kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_23_SPAdes.2kcontigs Assembled into 1309 contigs. Avg Length: 5326.9770817417875 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 943 -- 2000.0 to 5756.1 bp 218 -- 5756.1 to 9512.2 bp 70 -- 9512.2 to 13268.3 bp 46 -- 13268.3 to 17024.4 bp 15 -- 17024.4 to 20780.5 bp 8 -- 20780.5 to 24536.6 bp 4 -- 24536.6 to 28292.7 bp 1 -- 28292.7 to 32048.8 bp 2 -- 32048.8 to 35804.9 bp 2 -- 35804.9 to 39561.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1d 12h 10m 45s.
Objects
Created Object Name Type Description
DBSC_19_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_19_SPAdes.2Kcontigs Assembled into 1424 contigs. Avg Length: 7125.0667134831465 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 1107 -- 2001.0 to 9067.2 bp 187 -- 9067.2 to 16133.4 bp 68 -- 16133.4 to 23199.6 bp 33 -- 23199.6 to 30265.8 bp 17 -- 30265.8 to 37332.0 bp 5 -- 37332.0 to 44398.2 bp 2 -- 44398.2 to 51464.4 bp 0 -- 51464.4 to 58530.6 bp 4 -- 58530.6 to 65596.79999999999 bp 1 -- 65596.79999999999 to 72663.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 6h 6m 17s.
Objects
Created Object Name Type Description
DBSC_18_metaSPAdes.Assembly.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_18_metaSPAdes.Assembly.2Kcontigs Assembled into 567 contigs. Avg Length: 8396.072310405643 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 440 -- 2000.0 to 10648.7 bp 80 -- 10648.7 to 19297.4 bp 18 -- 19297.4 to 27946.100000000002 bp 11 -- 27946.100000000002 to 36594.8 bp 5 -- 36594.8 to 45243.5 bp 7 -- 45243.5 to 53892.200000000004 bp 3 -- 53892.200000000004 to 62540.90000000001 bp 0 -- 62540.90000000001 to 71189.6 bp 1 -- 71189.6 to 79838.3 bp 2 -- 79838.3 to 88487.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1d 9h 0m 58s.
Objects
Created Object Name Type Description
DBSC_17_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_17_SPAdes.2Kcontigs Assembled into 1596 contigs. Avg Length: 5780.0319548872185 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 1089 -- 2005.0 to 5806.3 bp 270 -- 5806.3 to 9607.6 bp 121 -- 9607.6 to 13408.900000000001 bp 56 -- 13408.900000000001 to 17210.2 bp 23 -- 17210.2 to 21011.5 bp 24 -- 21011.5 to 24812.800000000003 bp 6 -- 24812.800000000003 to 28614.100000000002 bp 4 -- 28614.100000000002 to 32415.4 bp 1 -- 32415.4 to 36216.700000000004 bp 2 -- 36216.700000000004 to 40018.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1d 6h 49m 13s.
Objects
Created Object Name Type Description
DBSC_16_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_16_SPAdes.2Kcontigs Assembled into 1207 contigs. Avg Length: 6914.106048053024 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 966 -- 2003.0 to 9255.6 bp 138 -- 9255.6 to 16508.2 bp 58 -- 16508.2 to 23760.800000000003 bp 23 -- 23760.800000000003 to 31013.4 bp 10 -- 31013.4 to 38266.0 bp 6 -- 38266.0 to 45518.600000000006 bp 2 -- 45518.600000000006 to 52771.200000000004 bp 0 -- 52771.200000000004 to 60023.8 bp 1 -- 60023.8 to 67276.4 bp 3 -- 67276.4 to 74529.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1d 0h 26m 52s.
Objects
Created Object Name Type Description
DBSC_14_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_14_SPAdes.2Kcontigs Assembled into 1147 contigs. Avg Length: 7741.4638186573675 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 793 -- 2005.0 to 7688.2 bp 170 -- 7688.2 to 13371.4 bp 79 -- 13371.4 to 19054.6 bp 48 -- 19054.6 to 24737.8 bp 32 -- 24737.8 to 30421.0 bp 14 -- 30421.0 to 36104.2 bp 4 -- 36104.2 to 41787.4 bp 2 -- 41787.4 to 47470.6 bp 3 -- 47470.6 to 53153.799999999996 bp 2 -- 53153.799999999996 to 58837.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 17h 45m 38s.
Objects
Created Object Name Type Description
DBSC_13_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_13_SPAdes.2Kcontigs Assembled into 560 contigs. Avg Length: 9375.776785714286 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 424 -- 2001.0 to 10725.0 bp 69 -- 10725.0 to 19449.0 bp 36 -- 19449.0 to 28173.0 bp 12 -- 28173.0 to 36897.0 bp 8 -- 36897.0 to 45621.0 bp 2 -- 45621.0 to 54345.0 bp 4 -- 54345.0 to 63069.0 bp 1 -- 63069.0 to 71793.0 bp 0 -- 71793.0 to 80517.0 bp 4 -- 80517.0 to 89241.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 3h 33m 36s.
Objects
Created Object Name Type Description
DBSC_12_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_12_SPAdes.2Kcontigs Assembled into 805 contigs. Avg Length: 13911.15155279503 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 679 -- 2009.0 to 26383.4 bp 84 -- 26383.4 to 50757.8 bp 26 -- 50757.8 to 75132.20000000001 bp 8 -- 75132.20000000001 to 99506.6 bp 5 -- 99506.6 to 123881.0 bp 1 -- 123881.0 to 148255.40000000002 bp 1 -- 148255.40000000002 to 172629.80000000002 bp 0 -- 172629.80000000002 to 197004.2 bp 0 -- 197004.2 to 221378.6 bp 1 -- 221378.6 to 245753.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 12h 25m 9s.
Objects
Created Object Name Type Description
DBSC_11_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_11_SPAdes.2Kcontigs Assembled into 9444 contigs. Avg Length: 5063.12346463363 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 9390 -- 2000.0 to 34081.6 bp 28 -- 34081.6 to 66163.2 bp 5 -- 66163.2 to 98244.79999999999 bp 3 -- 98244.79999999999 to 130326.4 bp 3 -- 130326.4 to 162408.0 bp 4 -- 162408.0 to 194489.59999999998 bp 3 -- 194489.59999999998 to 226571.19999999998 bp 3 -- 226571.19999999998 to 258652.8 bp 3 -- 258652.8 to 290734.39999999997 bp 2 -- 290734.39999999997 to 322816.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 12h 53m 28s.
Objects
Created Object Name Type Description
DBSC_10_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_10_SPAdes.2Kcontigs Assembled into 22696 contigs. Avg Length: 6349.968408530138 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 22550 -- 2000.0 to 68920.5 bp 95 -- 68920.5 to 135841.0 bp 22 -- 135841.0 to 202761.5 bp 8 -- 202761.5 to 269682.0 bp 7 -- 269682.0 to 336602.5 bp 8 -- 336602.5 to 403523.0 bp 1 -- 403523.0 to 470443.5 bp 4 -- 470443.5 to 537364.0 bp 0 -- 537364.0 to 604284.5 bp 1 -- 604284.5 to 671205.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 12h 54m 57s.
Objects
Created Object Name Type Description
DBSC_08_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_08_SPAdes.2Kcontigs Assembled into 11193 contigs. Avg Length: 4770.283748771553 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 11144 -- 2000.0 to 72714.9 bp 21 -- 72714.9 to 143429.8 bp 15 -- 143429.8 to 214144.69999999998 bp 3 -- 214144.69999999998 to 284859.6 bp 5 -- 284859.6 to 355574.5 bp 1 -- 355574.5 to 426289.39999999997 bp 2 -- 426289.39999999997 to 497004.29999999993 bp 1 -- 497004.29999999993 to 567719.2 bp 0 -- 567719.2 to 638434.1 bp 1 -- 638434.1 to 709149.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 14h 54m 58s.
Objects
Created Object Name Type Description
DBSC_07_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBSC_07_SPAdes.2Kcontigs Assembled into 28996 contigs. Avg Length: 5546.557042350669 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 28963 -- 2000.0 to 147076.6 bp 17 -- 147076.6 to 292153.2 bp 8 -- 292153.2 to 437229.80000000005 bp 4 -- 437229.80000000005 to 582306.4 bp 1 -- 582306.4 to 727383.0 bp 1 -- 727383.0 to 872459.6000000001 bp 1 -- 872459.6000000001 to 1017536.2000000001 bp 0 -- 1017536.2000000001 to 1162612.8 bp 0 -- 1162612.8 to 1307689.4000000001 bp 1 -- 1307689.4000000001 to 1452766.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1h 9m 12s.
Objects
Created Object Name Type Description
DBAT_13_metaSPAdes.Assembly.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBAT_13_metaSPAdes.Assembly.2Kcontigs Assembled into 696 contigs. Avg Length: 8337.613505747126 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 682 -- 2000.0 to 63114.8 bp 7 -- 63114.8 to 124229.6 bp 2 -- 124229.6 to 185344.40000000002 bp 1 -- 185344.40000000002 to 246459.2 bp 1 -- 246459.2 to 307574.0 bp 0 -- 307574.0 to 368688.80000000005 bp 0 -- 368688.80000000005 to 429803.60000000003 bp 1 -- 429803.60000000003 to 490918.4 bp 1 -- 490918.4 to 552033.2000000001 bp 1 -- 552033.2000000001 to 613148.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 12m 48s.
Objects
Created Object Name Type Description
DBAT_12_metaSPAdes.Assembly.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBAT_12_metaSPAdes.Assembly.2Kcontigs Assembled into 1637 contigs. Avg Length: 6884.14050091631 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 1605 -- 2001.0 to 40154.4 bp 12 -- 40154.4 to 78307.8 bp 10 -- 78307.8 to 116461.20000000001 bp 3 -- 116461.20000000001 to 154614.6 bp 2 -- 154614.6 to 192768.0 bp 3 -- 192768.0 to 230921.40000000002 bp 1 -- 230921.40000000002 to 269074.8 bp 0 -- 269074.8 to 307228.2 bp 0 -- 307228.2 to 345381.60000000003 bp 1 -- 345381.60000000003 to 383535.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1h 8m 56s.
Objects
Created Object Name Type Description
DBAT_11_metaSPAdes.Assembly.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBAT_11_metaSPAdes.Assembly.2Kcontigs Assembled into 998 contigs. Avg Length: 7220.244488977956 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 990 -- 2003.0 to 81950.2 bp 2 -- 81950.2 to 161897.4 bp 1 -- 161897.4 to 241844.59999999998 bp 1 -- 241844.59999999998 to 321791.8 bp 0 -- 321791.8 to 401739.0 bp 2 -- 401739.0 to 481686.19999999995 bp 0 -- 481686.19999999995 to 561633.4 bp 1 -- 561633.4 to 641580.6 bp 0 -- 641580.6 to 721527.7999999999 bp 1 -- 721527.7999999999 to 801475.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 22h 34m 1s.
Objects
Created Object Name Type Description
DBAT_05_metaSPAdes.Assembly.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBAT_05_metaSPAdes.Assembly.2Kcontigs Assembled into 614 contigs. Avg Length: 6600.413680781759 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 472 -- 2002.0 to 8170.1 bp 83 -- 8170.1 to 14338.2 bp 34 -- 14338.2 to 20506.300000000003 bp 15 -- 20506.300000000003 to 26674.4 bp 6 -- 26674.4 to 32842.5 bp 1 -- 32842.5 to 39010.600000000006 bp 0 -- 39010.600000000006 to 45178.700000000004 bp 1 -- 45178.700000000004 to 51346.8 bp 1 -- 51346.8 to 57514.9 bp 1 -- 57514.9 to 63683.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 3d 2h 15m 51s.
Objects
Created Object Name Type Description
DBAT_04_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBAT_04_SPAdes.2Kcontigs Assembled into 1270 contigs. Avg Length: 6209.604724409449 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 1052 -- 2001.0 to 8834.0 bp 120 -- 8834.0 to 15667.0 bp 54 -- 15667.0 to 22500.0 bp 25 -- 22500.0 to 29333.0 bp 10 -- 29333.0 to 36166.0 bp 6 -- 36166.0 to 42999.0 bp 2 -- 42999.0 to 49832.0 bp 0 -- 49832.0 to 56665.0 bp 0 -- 56665.0 to 63498.0 bp 1 -- 63498.0 to 70331.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 2h 59m 56s.
Objects
Created Object Name Type Description
DBAT_03_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBAT_03_SPAdes.2Kcontigs Assembled into 908 contigs. Avg Length: 8597.454845814978 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 542 -- 2001.0 to 7123.4 bp 161 -- 7123.4 to 12245.8 bp 90 -- 12245.8 to 17368.199999999997 bp 59 -- 17368.199999999997 to 22490.6 bp 26 -- 22490.6 to 27613.0 bp 17 -- 27613.0 to 32735.399999999998 bp 4 -- 32735.399999999998 to 37857.799999999996 bp 4 -- 37857.799999999996 to 42980.2 bp 2 -- 42980.2 to 48102.6 bp 3 -- 48102.6 to 53225.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 1d 3h 5m 34s.
Objects
Created Object Name Type Description
DBAT_02_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBAT_02_SPAdes.2Kcontigs Assembled into 672 contigs. Avg Length: 11028.144345238095 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 583 -- 2008.0 to 21868.6 bp 57 -- 21868.6 to 41729.2 bp 20 -- 41729.2 to 61589.799999999996 bp 3 -- 61589.799999999996 to 81450.4 bp 3 -- 81450.4 to 101311.0 bp 2 -- 101311.0 to 121171.59999999999 bp 1 -- 121171.59999999999 to 141032.19999999998 bp 2 -- 141032.19999999998 to 160892.8 bp 0 -- 160892.8 to 180753.4 bp 1 -- 180753.4 to 200614.0 bp
Links
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 7h 51m 16s.
Objects
Created Object Name Type Description
DBAT_01_SPAdes.2Kcontigs Assembly Assembled contigs
Summary
Assembly saved to: alvaro_munoz:narrative_1620781316072/DBAT_01_SPAdes.2Kcontigs Assembled into 326 contigs. Avg Length: 10507.42944785276 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 242 -- 2010.0 to 13524.4 bp 50 -- 13524.4 to 25038.8 bp 27 -- 25038.8 to 36553.2 bp 4 -- 36553.2 to 48067.6 bp 2 -- 48067.6 to 59582.0 bp 0 -- 59582.0 to 71096.4 bp 0 -- 71096.4 to 82610.8 bp 0 -- 82610.8 to 94125.2 bp 0 -- 94125.2 to 105639.59999999999 bp 1 -- 105639.59999999999 to 117154.0 bp
Links

STEP 003 - Confirm quality of filtered/trimmed reads with FastQC...

NOTE 1: DBSC_15, DBSC_20, DBSC_21, DBSC_22, and DBSC_24 did not pass the QC to be assembled nor to assign taxonomy of their unassembled reads

NOTE 2: SONST2_7000m, SONST4_7000m, DBAT_10, DBAT_11, DBAT_12, DBAT_13, and DBSC_31 reads uploaded to this Kbase narrative were already high-quality reads (see their corresponding FastQC report in "STEP 002"). Thus, they were not processed through Trimmomatic in Kbase.

A quality control application for high throughput sequence data.
This app completed without errors in 8m 8s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_30_pos-trimmed.fastq.gz_paired_90888_210_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_30_pos-trimmed.fastq.gz_paired_90888_210_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 8m 20s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_29_pos-trimmed.fastq.gz_paired_90888_198_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_29_pos-trimmed.fastq.gz_paired_90888_198_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 3m 50s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_28_pos-trimmed.fastq.gz_paired_90888_202_2.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_28_pos-trimmed.fastq.gz_paired_90888_202_2.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 15s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_27_pos-trimmed.fastq.gz_paired_90888_194_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_27_pos-trimmed.fastq.gz_paired_90888_194_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 7m 60s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_26_pos-trimmed.fastq.gz_paired_90888_190_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_26_pos-trimmed.fastq.gz_paired_90888_190_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 5m 53s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_25_pos-trimmed.fastq.gz_paired_90888_186_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_25_pos-trimmed.fastq.gz_paired_90888_186_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 9m 23s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_24_pos-trimmed.fastq.gz_paired_90888_839_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_24_pos-trimmed.fastq.gz_paired_90888_839_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 7m 29s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_23_pos-trimmed.fastq.gz_paired_90888_292_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_23_pos-trimmed.fastq.gz_paired_90888_292_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 8m 14s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_19_pos-trimmed.fastq.gz_paired_90888_300_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_19_pos-trimmed.fastq.gz_paired_90888_300_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 31s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_18_Trimmomatic_v1_paired_90888_372_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_18_Trimmomatic_v1_paired_90888_372_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 8m 17s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_17_pos-trimmed.fastq.gz_paired_90888_316_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_17_pos-trimmed.fastq.gz_paired_90888_316_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 5m 21s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_16_pos-trimmed.fastq.gz_paired_90888_295_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_16_pos-trimmed.fastq.gz_paired_90888_295_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 10m 49s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_14_pos-trimmed.fastq.gz_paired_90888_303_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_14_pos-trimmed.fastq.gz_paired_90888_303_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 12s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_13_pos-trimmed.fastq.gz_paired_90888_308_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_13_pos-trimmed.fastq.gz_paired_90888_308_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 10m 38s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_12_pos-trimmed.fastq.gz_paired_90888_203_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_12_pos-trimmed.fastq.gz_paired_90888_203_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 8m 19s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_11_pos-trimmed.fastq.gz_paired_90888_226_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_11_pos-trimmed.fastq.gz_paired_90888_226_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 15m 18s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_10_pos-trimmed.fastq.gz_paired_90888_218_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_10_pos-trimmed.fastq.gz_paired_90888_218_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 8m 1s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_08_pos-trimmed.fastq.gz_paired_90888_214_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_08_pos-trimmed.fastq.gz_paired_90888_214_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 12m 10s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_07_pos-trimmed.fastq.gz_paired_90888_222_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_07_pos-trimmed.fastq.gz_paired_90888_222_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 14s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_5_Trimmomatic_v1_paired_90888_371_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_5_Trimmomatic_v1_paired_90888_371_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 22m 30s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_04_pos-trimmed.fastq.gz_paired_90888_312_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_04_pos-trimmed.fastq.gz_paired_90888_312_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 4m 46s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_03_pos-trimmed.fastq.gz_paired_90888_252_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_03_pos-trimmed.fastq.gz_paired_90888_252_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 20m 11s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_02_pos-trimmed.fastq.gz_paired_90888_182_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_02_pos-trimmed.fastq.gz_paired_90888_182_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 47s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_01_pos-trimmed.fastq.gz_paired_90888_260_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_01_pos-trimmed.fastq.gz_paired_90888_260_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 8m 25s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DB_SORT_pos-trimmed.fastq.gz_paired_90888_178_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DB_SORT_pos-trimmed.fastq.gz_paired_90888_178_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report

STEP 002 - Quality filter and trim raw reads with Trimmomatic

Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 28m 31s.
Objects
Created Object Name Type Description
DB_SORT_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DB_SORT_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DB_SORT_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 5m 29s.
Objects
Created Object Name Type Description
DBAT_01_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBAT_01_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBAT_01_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 7m 52s.
Objects
Created Object Name Type Description
DBAT_02_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBAT_02_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBAT_02_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 32m 58s.
Objects
Created Object Name Type Description
DBAT_03_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBAT_03_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBAT_03_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 49m 52s.
Objects
Created Object Name Type Description
DBAT_04_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBAT_04_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBAT_04_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 43m 15s.
Objects
Created Object Name Type Description
DBAT_05_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBAT_05_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBAT_05_pos-trimmed.fastq.gz_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 7m 49s.
Objects
Created Object Name Type Description
DBSC_07_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_07_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_07_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 40m 4s.
Objects
Created Object Name Type Description
DBSC_08_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_08_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_08_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 49m 33s.
Objects
Created Object Name Type Description
DBSC_10_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_10_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_10_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 51m 55s.
Objects
Created Object Name Type Description
DBSC_11_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_11_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_11_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 44m 41s.
Objects
Created Object Name Type Description
DBSC_12_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_12_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_12_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 57m 14s.
Objects
Created Object Name Type Description
DBSC_13_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_13_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_13_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 50m 48s.
Objects
Created Object Name Type Description
DBSC_14_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_14_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_14_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 6m 40s.
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 34m 9s.
Objects
Created Object Name Type Description
DBSC_16_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_16_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_16_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1d 21h 43m 39s.
Objects
Created Object Name Type Description
DBSC_17_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_17_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_17_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 37m 42s.
Objects
Created Object Name Type Description
DBSC_18_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_18_Trimmomatic_v1_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_18_Trimmomatic_v1_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 44m 50s.
Objects
Created Object Name Type Description
DBSC_19_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_19_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_19_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 4m 37s.
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 6m 37s.
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 4m 38s.
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 27m 45s.
Objects
Created Object Name Type Description
DBSC_23_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_23_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_23_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 18m 34s.
Objects
Created Object Name Type Description
DBSC_24_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_24_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_24_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 38m 59s.
Objects
Created Object Name Type Description
DBSC_25_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_25_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_25_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 44m 7s.
Objects
Created Object Name Type Description
DBSC_26_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_26_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_26_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 43m 28s.
Objects
Created Object Name Type Description
DBSC_27_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_27_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_27_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 31m 12s.
Objects
Created Object Name Type Description
DBSC_28_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_28_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_28_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 32m 17s.
Objects
Created Object Name Type Description
DBSC_29_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_29_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_29_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 44m 5s.
Objects
Created Object Name Type Description
DBSC_30_pos-trimmed.fastq.gz_paired PairedEndLibrary Trimmed Reads
DBSC_30_pos-trimmed.fastq.gz_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
DBSC_30_pos-trimmed.fastq.gz_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
A quality control application for high throughput sequence data.
This app completed without errors in 10m 57s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DB_SORT_01_S31_L001_R1_001.fastq.gz_reads_90888_158_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DB_SORT_01_S31_L001_R1_001.fastq.gz_reads_90888_158_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 16s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_31_S2_L001_R1_001.fastq.gz_reads_90888_483_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_31_S2_L001_R1_001.fastq.gz_reads_90888_483_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 8m 27s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_30_S30_L001_R1_001.fastq.gz_reads_90888_98_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_30_S30_L001_R1_001.fastq.gz_reads_90888_98_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 8m 33s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_29_S29_L001_R1_001.fastq.gz_reads_90888_115_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_29_S29_L001_R1_001.fastq.gz_reads_90888_115_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 7m 53s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_28_S28_L001_R1_001.fastq.gz_reads_90888_100_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_28_S28_L001_R1_001.fastq.gz_reads_90888_100_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 37s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_27_S27_L001_R1_001.fastq.gz_reads_90888_86_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_27_S27_L001_R1_001.fastq.gz_reads_90888_86_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 8m 36s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_26_S26_L001_R1_001.fastq.gz_reads_90888_91_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_26_S26_L001_R1_001.fastq.gz_reads_90888_91_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 14m 25s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_25_S25_L001_R1_001.fastq.gz_reads_90888_66_2.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_25_S25_L001_R1_001.fastq.gz_reads_90888_66_2.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 19m 47s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_24_S24_L001_R1_001.fastq.gz_reads_90888_56_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_24_S24_L001_R1_001.fastq.gz_reads_90888_56_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 26s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_23_S23_L001_R1_001.fastq.gz_reads_90888_54_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_23_S23_L001_R1_001.fastq.gz_reads_90888_54_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 21s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_22_S22_L001_R1_001.fastq.gz_reads_90888_63_2.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_22_S22_L001_R1_001.fastq.gz_reads_90888_63_2.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 15m 53s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_21_S21_L001_R1_001.fastq.gz_reads_90888_113_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_21_S21_L001_R1_001.fastq.gz_reads_90888_113_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 7s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_20_S20_L001_R1_001.fastq.gz_reads_90888_82_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_20_S20_L001_R1_001.fastq.gz_reads_90888_82_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 17s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_19_S19_L001_R1_001.fastq.gz_reads_90888_109_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_19_S19_L001_R1_001.fastq.gz_reads_90888_109_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 19m 50s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_18_S18_L001_R1_001.fastq.gz_reads_90888_75_2.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_18_S18_L001_R1_001.fastq.gz_reads_90888_75_2.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 16m 37s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_17_S17_L001_R1_001.fastq.gz_reads_90888_47_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_17_S17_L001_R1_001.fastq.gz_reads_90888_47_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 10m 45s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_16_S16_L001_R1_001.fastq.gz_reads_90888_42_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_16_S16_L001_R1_001.fastq.gz_reads_90888_42_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 17m 21s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_15_S15_L001_R1_001.fastq.gz_reads_90888_95_3.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_15_S15_L001_R1_001.fastq.gz_reads_90888_95_3.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 12m 9s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_14_S14_L001_R1_001.fastq.gz_reads_90888_37_2.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_14_S14_L001_R1_001.fastq.gz_reads_90888_37_2.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 12m 58s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_13_S13_L001_R1_001.fastq.gz_reads_90888_60_2.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_13_S13_L001_R1_001.fastq.gz_reads_90888_60_2.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 10m 57s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_12_S12_L001_R1_001.fastq.gz_reads_90888_35_3.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_12_S12_L001_R1_001.fastq.gz_reads_90888_35_3.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 14m 48s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_11_S11_L001_R1_001.fastq.gz_reads_90888_25_3.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_11_S11_L001_R1_001.fastq.gz_reads_90888_25_3.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 15m 57s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_10_S10_L001_R1_001.fastq.gz_reads_90888_24_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_10_S10_L001_R1_001.fastq.gz_reads_90888_24_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 16s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_08_S8_L001_R1_001.fastq.gz_reads_90888_58_2.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_08_S8_L001_R1_001.fastq.gz_reads_90888_58_2.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 15m 20s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBSC_07_S7_L001_R1_001.fastq.gz_reads_90888_13_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBSC_07_S7_L001_R1_001.fastq.gz_reads_90888_13_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 5m 60s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_13_S3_L001_R1_001.fastq.gz_reads_90888_780_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_13_S3_L001_R1_001.fastq.gz_reads_90888_780_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 1m 32s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_12_S2_L001_R1_001.fastq.gz_reads_90888_774_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_12_S2_L001_R1_001.fastq.gz_reads_90888_774_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 1m 49s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_11_S1_L001_R1_001.fastq.gz_reads_90888_775_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_11_S1_L001_R1_001.fastq.gz_reads_90888_775_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 1m 50s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_10_-SORT_ctrl-_S1_L001_R1_001.fastq.gz_reads_90888_778_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_10_-SORT_ctrl-_S1_L001_R1_001.fastq.gz_reads_90888_778_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 11m 37s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_05_S5_L001_R1_001.fastq.gz_reads_90888_12_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_05_S5_L001_R1_001.fastq.gz_reads_90888_12_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 18m 54s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_04_S4_L001_R1_001.fastq.gz_reads_90888_8_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_04_S4_L001_R1_001.fastq.gz_reads_90888_8_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 10m 53s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_03_S3_L001_R1_001.fastq.gz_reads_90888_49_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_03_S3_L001_R1_001.fastq.gz_reads_90888_49_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 15m 50s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_02_S2_L001_R1_001.fastq.gz_reads_90888_4_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_02_S2_L001_R1_001.fastq.gz_reads_90888_4_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 16m 33s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DBAT_01_S1_L001_R1_001.fastq.gz_reads_90888_52_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DBAT_01_S1_L001_R1_001.fastq.gz_reads_90888_52_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 10m 39s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • DB_SORT_01_S31_L001_R1_001.fastq.gz_reads_90888_158_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • DB_SORT_01_S31_L001_R1_001.fastq.gz_reads_90888_158_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 42m 55s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • SONST2_02_7000m.fastq.gz_90888_1130_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • SONST2_02_7000m.fastq.gz_90888_1130_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
A quality control application for high throughput sequence data.
This app completed without errors in 44m 48s.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/90888
  • SONST4_7000m.fastq.gz_90888_1132_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • SONST4_7000m.fastq.gz_90888_1132_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_batch(
    [{
        "app_id": "kb_uploadmethods/import_fastq_noninterleaved_as_reads_from_staging",
        "tag": "release",
        "version": "5b9346463df88a422ff5d4f4cba421679f63c73f",
        "params": [{
            "fastq_fwd_staging_file_name": "SONST2_02_7000_R1_clean.fastq.gz",
            "fastq_rev_staging_file_name": "SONST2_02_7000_R2_clean.fastq.gz",
            "name": "SONST2_02_7000m.fastq.gz"
        }],
        "shared_params": {
            "sequencing_tech": "Illumina",
            "single_genome": 1,
            "read_orientation_outward": 0,
            "insert_size_std_dev": None,
            "insert_size_mean": None
        }
    }],
    cell_id="650d2d7e-ef18-4eb6-843f-7ea4de48e8ab",
    run_id="04d86bba-4063-4ad2-853b-d71e0ce52f85"
)
from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_batch(
    [{
        "app_id": "kb_uploadmethods/import_fastq_noninterleaved_as_reads_from_staging",
        "tag": "release",
        "version": "5b9346463df88a422ff5d4f4cba421679f63c73f",
        "params": [{
            "fastq_fwd_staging_file_name": "SONST4_02_7000_R1_clean.fastq.gz",
            "fastq_rev_staging_file_name": "SONST4_02_7000_R2_clean.fastq.gz",
            "name": "SONST4_7000m.fastq.gz"
        }],
        "shared_params": {
            "sequencing_tech": "Illumina",
            "single_genome": 1,
            "read_orientation_outward": 0,
            "insert_size_std_dev": None,
            "insert_size_mean": None
        }
    }],
    cell_id="0e6aea25-8e9f-4409-bb68-3331faa57352",
    run_id="bf51af5f-fa0a-4819-b099-44e320e10d44"
)

Deep-sea microbiomes sampled with traditional or pressure-retaining instrumentation

A fundamental property of life in the sea is that with increasing depth must come increased adaptation to elevated hydrostatic pressures. This project aims to assess technology for the accurate characterization of microbial biodiversity and biochemistry at greater depths, and validate its use in some of the deepest and least-explored waters in the Ocean: Hadal Trench. Compared to the 0.1 megapascal (MPa) of surface waters, organisms inhabiting at the average depth of the Ocean (3800 m) have to deal with pressures of 38 MPa (5,500 psi). The effects of these high pressure have been most thoroughly investigated in microorganisms, where it has been found to affect membrane integrity and transport, cytoskeletal assembly and both DNA and protein synthesis. We will explore the diversity and activity of microorganisms from 2000 m to >8,000 m depths within the highly productive water column of hadal trenches, comparing seawater samples obtained with and without substantial pressure changes during recovery. A pressure retaining device was used to sample the microbial communities of the watercolumn with reduced decompression during retreival (Peoples et. al., 2019).

References: Peoples LM, Norenberg M, Price D, McGoldrick M, Novotny M, Bochdansky A, Bartlett DH. A full-ocean-depth rated modular lander and pressure-retaining sampler capable of collecting hadal-endemic microbes under in situ conditions. Deep Sea Research Part I: Oceanographic Research Papers. 2019 Jan 1;143:50-7.

STEP 001 - Uploaded Atacama Trench and San Clemente Basin metagenome raw fastQs

Released Apps

  1. Annotate Microbial Assembly with RASTtk - v1.073
    • [1] Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. 2008;9: 75. doi:10.1186/1471-2164-9-75
    • [2] Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al.vThe SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206 D214. doi:10.1093/nar/gkt1226
    • [3] Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5. doi:10.1038/srep08365
    • [4] Kent WJ. BLAT The BLAST-Like Alignment Tool. Genome Res. 2002;12: 656 664. doi:10.1101/gr.229202
    • [5] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389-3402. doi:10.1093/nar/25.17.3389
    • [6] Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25: 955 964.
    • [7] Cobucci-Ponzano B, Rossi M, Moracci M. Translational recoding in archaea. Extremophiles. 2012;16: 793 803. doi:10.1007/s00792-012-0482-8
    • [8] Meyer F, Overbeek R, Rodriguez A. FIGfams: yet another set of protein families. Nucleic Acids Res. 2009;37 6643-54. doi:10.1093/nar/gkp698.
    • [9] van Belkum A, Sluijuter M, de Groot R, Verbrugh H, Hermans PW. Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. J Clin Microbiol. 1996;34: 1176 1179.
    • [10] Croucher NJ, Vernikos GS, Parkhill J, Bentley SD. Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics. 2011;12: 120. doi:10.1186/1471-2164-12-120
    • [11] Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11: 119. doi:10.1186/1471-2105-11-119
    • [12] Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23: 673 679. doi:10.1093/bioinformatics/btm009
    • [13] Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 2012;40: e126. doi:10.1093/nar/gks406
  2. Annotate Multiple Microbial Assemblies with RASTtk - v1.073
    • [1] Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. 2008;9: 75. doi:10.1186/1471-2164-9-75
    • [2] Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206 D214. doi:10.1093/nar/gkt1226
    • [3] Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5. doi:10.1038/srep08365
    • [4] Kent WJ. BLAT The BLAST-Like Alignment Tool. Genome Res. 2002;12: 656 664. doi:10.1101/gr.229202
    • [5] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389-3402. doi:10.1093/nar/25.17.3389
    • [6] Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25: 955 964.
    • [7] Cobucci-Ponzano B, Rossi M, Moracci M. Translational recoding in archaea. Extremophiles. 2012;16: 793 803. doi:10.1007/s00792-012-0482-8
    • [8] Meyer F, Overbeek R, Rodriguez A. FIGfams: yet another set of protein families. Nucleic Acids Res. 2009;37 6643-54. doi:10.1093/nar/gkp698.
    • [9] van Belkum A, Sluijuter M, de Groot R, Verbrugh H, Hermans PW. Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. J Clin Microbiol. 1996;34: 1176 1179.
    • [10] Croucher NJ, Vernikos GS, Parkhill J, Bentley SD. Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics. 2011;12: 120. doi:10.1186/1471-2164-12-120
    • [11] Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11: 119. doi:10.1186/1471-2105-11-119
    • [12] Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23: 673 679. doi:10.1093/bioinformatics/btm009
    • [13] Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 2012;40: e126. doi:10.1093/nar/gks406
  3. Assemble Reads with metaSPAdes - v3.15.3
    • Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017; 27:824 834. doi: 10.1101/gr.213959.116
    • Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo Assembler. Curr Protoc Bioinformatics. 2020 Jun;70(1):e102. doi: 10.1002/cpbi.102.
  4. Assess Genome Quality with CheckM - v1.0.18
    • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25: 1043 1055. doi:10.1101/gr.186072.114
    • CheckM source:
    • Additional info:
  5. Assess Read Quality with FastQC - v0.12.1
    • FastQC source: Bioinformatics Group at the Babraham Institute, UK.
  6. Bin Contigs using CONCOCT - v1.1
    • Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C. Binning metagenomic contigs by coverage and composition. Nature Methods. 2014;11: 1144-1146. doi:10.1038/nmeth.3103
    • CONCOCT source:
  7. Bin Contigs using MaxBin2 - v2.2.4
    • Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32: 605 607. doi:10.1093/bioinformatics/btv638 (2) 1. Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2: 26. doi:10.1186/2049-2618-2-26
    • Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2: 26. doi:10.1186/2049-2618-2-26
    • Maxbin2 source:
    • Maxbin source:
  8. Build ReadsSet - v1.7.6
    • Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, Henry CS, Arkin AP. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
  9. Classify Microbes with GTDB-Tk - v2.3.2
    • Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, Volume 38, Issue 23, 1 December 2022, Pages 5315 5316. DOI: https://doi.org/10.1093/bioinformatics/btac672
    • Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks, GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database, Bioinformatics, Volume 36, Issue 6, 15 March 2020, Pages 1925 1927. DOI: https://doi.org/10.1093/bioinformatics/btz848
    • Donovan H Parks, Maria Chuvochina, Christian Rinke, Aaron J Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D785 D794. DOI: https://doi.org/10.1093/nar/gkab776
    • Parks, D., Chuvochina, M., Waite, D. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36, 996 1004 (2018). DOI: https://doi.org/10.1038/nbt.4229
    • Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol. 2020;10.1038/s41587-020-0501-8. DOI:10.1038/s41587-020-0501-8
    • Rinke C, Chuvochina M, Mussig AJ, Chaumeil PA, Dav n AA, Waite DW, Whitman WB, Parks DH, and Hugenholtz P. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol. 2021 Jul;6(7):946-959. DOI:10.1038/s41564-021-00918-8
    • Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, Henry CS, Arkin AP. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x
    • Matsen FA, Kodner RB, Armbrust EV. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics. 2010;11:538. Published 2010 Oct 30. doi:10.1186/1471-2105-11-538
    • Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114. Published 2018 Nov 30. DOI:10.1038/s41467-018-07641-9
    • Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119. Published 2010 Mar 8. DOI:10.1186/1471-2105-11-119
    • Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490. Published 2010 Mar 10. DOI:10.1371/journal.pone.0009490 link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835736/
    • Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7(10):e1002195. DOI:10.1371/journal.pcbi.1002195
    • Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016 Jun 20;17(1):132. DOI: 10.1186/s13059-016-0997-x
  10. Classify Taxonomy of Metagenomic Reads with Kaiju - v1.9.0
    • Chivian D, et al. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2023 Jan;18(1):208-238. doi: 10.1038/s41596-022-00747-x
    • Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016;7: 11257. doi:10.1038/ncomms11257
    • Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011;12: 385. doi:10.1186/1471-2105-12-385
    • Kaiju Homepage:
    • Kaiju DBs from:
    • Github for Kaiju:
    • Krona homepage:
    • Github for Krona:
  11. Compare Assembled Contig Distributions - v1.1.2
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
  12. Extract Bins as Assemblies from BinnedContigs - v1.0.2
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
  13. Insert Genome Into SpeciesTree - v2.2.0
    • Price MN, Dehal PS, Arkin AP. FastTree 2 Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5. doi:10.1371/journal.pone.0009490
  14. Insert Set of Genomes Into SpeciesTree - v2.2.0
    • Price MN, Dehal PS, Arkin AP. FastTree 2 Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5. doi:10.1371/journal.pone.0009490
  15. Merge Reads Libraries - v1.2.2
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
  16. MetaBAT2 Contig Binning - v1.7
    • Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3: e1165. doi:10.7717/peerj.1165
    • MetaBAT2 source:
  17. Optimize Bacterial or Archaeal Binned Contigs using DAS Tool - v1.1.2
    • Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. 2018; 3(7): 836-843. doi:10.1038/s41564-018-0171-1
    • DAS_Tool source:
    • Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11: 119. doi:10.1186/1471-2105-11-119
    • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10: 421. doi:10.1186/1471-2105-10-421
    • Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nature Methods. 2015;12: 59-60. doi:10.1038/nmeth.3176
    • Pullseq:
    • R: A Language and Environment for Statistical Computing:
    • Ruby: A Programmers Best Friend:
  18. Trim Reads with Trimmomatic - v0.36
    • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30: 2114 2120. doi:10.1093/bioinformatics/btu170

Apps in Beta

  1. Build Microbial SpeciesTree - v1.6.0
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163