MetaCerberus Tutorial - What’s in the Results folder?

Now that we’ve run the MetaCerberus pipeline, let’s take a look at the results folder. Having ran the --super option on my data, the results folder looks like so:

Now a closer look at each subdirectory of our results:

Step_5-format:

Step 5 contents only consist of a complete file, which merely indicates Step 5 ran to completion.

Step_6-metaomeQC

Here are the contents of step_06-metaomeQC:

The file read-stats.txt contains statistics for your input file, like so:

Note

The file stderr.out is a log file where any error messages will be stored.

Step_7-geneCall

Contents of the step_07-geneCall directory are:

These are protein files in different formats.

Step_8-hmmer

Contents of the step_08-hmmer directory are:

For your MetaCerberus run, you should get a subdirectory for the mode that MetaCerberus used (FragGeneScan, Prodigal, Prodigalgv, etc). In this example run, we have several file outputs for FragGeneScan. The types of outputs are similar for prodigal.

• Quick link to examples:

  • KOFam_all_FOAM-FragGeneScan_Lambda_phage_sequences.tsv

  • KOFam_all_KEGG-FragGeneScan_Lambda_phage_sequences.tsv

  • filtered-KOFam_all_FOAM.tsv

  • filtered-KOFam_all_KEGG.tsv

  • filtered.tsv

This is what they look like:

Note

.tsv files can be opened with Excel.

KOFam_all_FOAM-FragGeneScan_Lambda_phage_sequences.tsv:

KOFam_all_KEGG-FragGeneScan_Lambda_phage_sequences.tsv

filtered-KOFam_all_FOAM.tsv

filtered-KOFam_all_KEGG.tsv

filtered.tsv

Step_9-parse

The contents of step_09-parse are:

• Quick link to examples:

  • HMMER-KOFam_all_FOAM_top_5.tsv

  • HMMER-KOFam_all_KEGG_top_5.tsv

  • HMMER_BH_KOFam_all_FOAM_rollup2.tsv

  • HMMER_BH_KOFam_all_KEGG_rollup2.tsv

  • HMMER_top_5.tsv

  • KOFam_all_FOAM-rollup_counts.tsv

  • KOFam_all_KEGG-rollup_counts.tsv

  • counts_KOFam_all_FOAM.tsv

  • counts_KOFam_all_KEGG.tsv

  • top_5-FragGeneScan_Lambda_phage_sequences.tsv

Looking a little closer:

HMMER-KOFam_all_FOAM_top_5.tsv

HMMER-KOFam_all_KEGG_top_5.tsv

HMMER_BH_KOFam_all_FOAM_rollup2.tsv

HMMER_BH_KOFam_all_KEGG_rollup2.tsv

HMMER_top_5.tsv

KOFam_all_FOAM-rollup_counts.tsv

KOFam_all_KEGG-rollup_counts.tsv

counts_KOFam_all_FOAM.tsv

counts_KOFam_all_KEGG.tsv

top_5-FragGeneScan_Lambda_phage_sequences.tsv

Step_10-visualizeData

The contents of step_10-visualizeData are:

What’s in the FragGeneScan and Prodigal subdirectories?

Files under FragGeneScan or Prodigal:

• Quick link to examples:

  • KOFam_all_FOAM_level-1.S9-top5_FGS_tsv

  • KOFam_all_FOAM_level-2.tsv

  • KOFam_all_FOAM_level-3.tsv

  • KOFam_all_FOAM_level-4.tsv

  • KOFam_all_FOAM_level-id.tsv

  • KOFam_all_KEGG_level-1.tsv

  • KOFam_all_KEGG_level-2.tsv

  • KOFam_all_KEGG_level-3.tsv

  • KOFam_all_KEGG_level-id.tsv

  • fasta_stats.txt

  • sunburst_KOFam_all_FOAM.html

  • sunburst_KOFam_all_KEGG.html

KOFam_all_FOAM_level-1.tsv

KOFam_all_FOAM_level-2.tsv

KOFam_all_FOAM_level-3.tsv

KOFam_all_FOAM_level-4.tsv

KOFam_all_FOAM_level-id.tsv

KOFam_all_KEGG_level-1.tsv

KOFam_all_KEGG_level-2.tsv

KOFam_all_KEGG_level-3.tsv

KOFam_all_KEGG_level-id.tsv

fasta_stats.txt

sunburst_KOFam_all_FOAM.html — open in web browser

sunburst_KOFam_all_KEGG.html — open in web browser

Contents under combined:

At a glance:

• Quick link to examples:

  • counts_KOFam_all_FOAM.tsv

  • counts_KOFam_all_KEGG.tsv

  • stats.html

  • stats.tsv

  • img subdirectory

counts_KOFam_all_FOAM.tsv

counts_KOFam_all_KEGG.tsv

stats.html — open in web browser

stats.tsv

img — contains the individual .png image files which are collectively located in stats.html

Final

The contents of final are:

• There’s two .gbk files which are in GenBank Format.

• The ./final/fasta subdirectory contains .faa, .ffn, and .fna files of FragGeneScan, Prodigal, etc (depending on commands given):

---

• .faa - Protein FASTA file of the translated CDS/ORFs sequences

• .ffn - FASTA Feature Nucleotide file, the Nucleotide sequence of translated CDS/ORFs.

• .fna - Nucleotide FASTA file of the input contig sequences.

• The ./final/gff contains .gff and .gtf files:

---

• .gff - General Feature Format

• .gtf - Gene Transfer Format

What’s in the ./final/FragGeneScan_<file_name> and ./final/prodigal_<file_name> subdirectories?

A closer look:

• Quick link to examples:

  • HMMER_top_5.tsv

  • annotation_summary_KOFam_all_FOAM.tsv

  • annotation_summary_KOFam_all_KEGG.tsv

  • final_annotation_summary.tsv

  • rollup_KOFam_all_FOAM.tsv

  • rollup_KOFam_all_KEGG.tsv

HMMER_top_5.tsv

annotation_summary_KOFam_all_FOAM.tsv

annotation_summary_KOFam_all_KEGG.tsv

final_annotation_summary.tsv

rollup_KOFam_all_FOAM.tsv

rollup_KOFam_all_KEGG.tsv