Frequently asked questions and troubleshooting
Recommended auxiliary files
Some tools may require or recommend additional files to the reference sequence files - such as taxonomy files - to execute.
We provide a list of required or recommended files, and which pipeline parameters to give them to here:
- bracken
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - (nucleotide) accession2taxid file (
--accession2taxid)
- taxonomy name dump file (
- centrifuge
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - nucl2taxid file (
--nucl2taxid)
- taxonomy name dump file (
- diamond
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - prot2taxid file (
--prot2taxid)
- taxonomy name dump file (
- ganon
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - genome sizes file (
--genomesizes)*
- taxonomy name dump file (
- kaiju (no additional files required)
- kraken2
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - (nucleotide) accession2taxid file (
--accession2taxid) - (optional) custom seqid2taxid file (
--nucl2taxid)
- taxonomy name dump file (
- krakenuniq
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - (nucleotide) accession2taxid file (
--accession2taxid)
- taxonomy name dump file (
- malt
- a MEGAN ‘mapDB’ mapping file (
--malt_mapdb)
- a MEGAN ‘mapDB’ mapping file (
* will be automatically downloaded if not supplied. You must supply this to the pipeline if on an offline cluster.
What should an X auxiliary file look like?
Some database building tools require additional files to be supplied to the pipeline. These are typically taxonomy files, and each are formatted in different ways.
names dump
This is a NCBI taxdump-style taxonomy file, that associates taxon IDs with human-readable names.
From NCBI, these would correspond to taxdmp.tar.gz from the NCBI Taxonomy FTP server.
Always refer to the NCBI taxdump README for the most up-to-date information.
It is formatted as a tab-pipe (\t|\t)-separated file with four columns but no header row.
| Column | Column Name* | Description |
|---|---|---|
| 1 | tax_id | The taxon ID |
| 2 | name_txt | The human-readable name of the taxon |
| 3 | unique name | The unique variant of the name if not unique |
| 4 | name class | The type or category of the name (e.g. scientific, common name, synonym) |
* Column names as defined in the taxdump README, however not used in the file itself
Example:
1 | all | | synonym |
1 | root | | scientific name |
2 | Bacteria | Bacteria <bacteria> | scientific name |
2 | bacteria | | blast name |
2 | eubacteria | | genbank common name |
2 | Monera | Monera <bacteria> | in-part |
2 | Procaryotae | Procaryotae <bacteria> | in-part |
2 | Prokaryotae | Prokaryotae <bacteria> | in-part |
2 | Prokaryota | Prokaryota <bacteria> | in-part |
2 | prokaryote | prokaryote <bacteria> | in-part |
2 | prokaryotes | prokaryotes <bacteria> | in-part |
712 | Pasteurellaceae Pohl 1981 | | authority |
712 | Pasteurellaceae | | scientific name |
724 | Haemophilus | | scientific name |
724 | Haemophilus Winslow et al. 1917 | | authority |nodes dump
This is a NCBI taxdump-style taxonomy file, that associates taxon IDs their taxonomic parent within the taxonomic hierarchy.
From NCBI, these would correspond to taxdmp.tar.gz from the NCBI Taxonomy FTP server.
Always refer to the NCBI taxdump README for the most up-to-date information.
It is formatted as a tab-pipe (\t|\t)-separated file with fourteen columns but no header row.
| Column | Column Name* | Description |
|---|---|---|
| 1 | tax_id | The taxon ID |
| 2 | parent tax_id | The taxon ID of the parent taxon |
| 3 | rank | The NCBI taxonomic rank of the taxon |
| 4 | embl code | The EMBL code for the taxon |
| 5 | division id | The NCBI division ID for the taxon (referring to diversion.dmp NCBI taxdump file not used in nf-core/createtaxdb) |
| 6 | inherited div flag | 1 (true) or 0 flag if taxon entry inherits division ID from taxonomic parent |
| 7 | genetic code id | The genetic code ID for the taxon (referring to gencode.dmp NCBI taxdump file not used in nf-core/createtaxdb) |
| 8 | inherited gc flag | 1 (true) or 0 flag if taxon entry inherits genetic code ID from taxonomic parent |
| 9 | mitochondrial genetic code | The mitochondrial genetic code ID for the taxon (referring to gencode.dmp NCBI taxdump file not used in nf-core/createtaxdb) |
| 10 | inherited mgc flag | 1 (true) or 0 flag if taxonomic entry inherits mitocondrial gencode from parent taxon |
| 11 | genbank hidden flag | 1 (true) or 0 flag indicating if name is suppressed in NCBI GenBank database |
| 13 | hidden subtree root flag node | 1 (true) or 0 flag indicating if there is any sequence data |
| 14 | comments | Comments about the taxon |
* Column names as defined in the taxdump README, however not used in the file itself
Example:
1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | |
712 | 135625 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
724 | 712 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
727 | 724 | species | HI | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified |
815 | 171549 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
816 | 815 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
817 | 816 | species | BF | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified |
976 | 68336 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
1239 | 1783272 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
1300 | 186826 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
1301 | 1300 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
1311 | 1301 | species | SA | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified |accession2taxid
An accession2taxid file is a file that maps database sequence accession IDs (e.g. NCBI GenBank) to their corresponding taxon IDs.
From NCBI, these would correspond to nucl_gb.accession2taxid.gz and prot.accession2taxid.gz from the NCBI taxonomy FTP server.
It is formatted as a four column tab-separated file with a header row.
| Column | Column Name | Description |
|---|---|---|
| 1 | accession | The accession ID of the sequence without a version - typically embedded as first part of a FASTA header entry (e.g. for >NC_012920 Homo sapiens mitochondrion, complete genome) the accession is NC_012829) |
| 2 | accesion.version | The full accession version of the accession with the version suffix (e.g. .1) |
| 3 | taxid | The taxon ID corresponding to the names/nodes.dmp |
| 4 | gi | The old-style (now deprecated) NCBI GenInfo Identifier |
Example:
accession accession.version taxid gi
NC_018507 CP003708.1 91844 401871806
NZ_CP019811 CP019811.1 1311 1328913993
NZ_CP069563 CP069563.1 817 1986148684
NZ_CP069564 CP069564.1 817 1986152744
NC_012920 J01415.2 9606 113200490
NZ_LS483480 LS483480.1 727 1403648431
MT192765 MT192765.1 694009 1821109001It’s important to note that you can have multiple accession numbers within a FASTA file (i.e., one per sequence in the file), therefore accession2taxid mapping files should ensure they reference all accession numbers that are present in the FASTA file.
The accession column should not include the accession version in the first column (i.e. 1)
nucl2taxid
An accession2taxid file is a file that maps database sequence accession IDs (e.g. NCBI GenBank) to their corresponding taxon IDs.
It is a simpler version of the accession2taxid file, and is formatted as a two column tab-separated file without a header row.
| Column | Column Name | Description |
|---|---|---|
| 1 | accession | The nucleotide accession ID with version of the sequence - typically embedded as first part of a FASTA header entry (e.g. for >NC_012920.1 Homo sapiens mitochondrion, complete genome) the accession is NC_012829.1) |
| 2 | taxon id | The corresponding taxonomy ID of the sequence |
Example:
NC_012920.1 9606
MT192765.1 694009
NZ_CP069563.1 817
NC_018507.1 91844
NZ_CP019811 1311
NZ_LS483480.1 727
prot2taxid
An accession2taxid file is a file that maps database sequence accession IDs (e.g. NCBI GenBank) to their corresponding taxon IDs.
It is a simpler version of the accession2taxid file, and is formatted as a two column tab-separated file with a header row.
| Column | Column Name | Description |
|---|---|---|
| 1 | accession.version | The protein accession ID with version of the sequence - typically embedded as first part of a FASTA header entry (e.g. for >NC_012920.1 Homo sapiens mitochondrion, complete genome) the accession is NC_012829.1) |
| 2 | taxid | The corresponding taxonomy ID of the sequence |
Example:
accession.version taxid
QIK50426.1 694009
QIK50427.1 694009
QIK50428.1 694009
QIK50429.1 694009
QIK50430.1 694009
QIK50431.1 694009
QIK50432.1 694009
QIK50433.1 694009
QIK50434.1 694009
QIK50435.1 694009
QIK50436.1 694009
WP_000002661.1 1311
WP_000002812.1 1311
WP_000003859.1 1311genome sizes file
A genome sizes file is a file that maps taxonomy IDs to their estimated genome file size.
This file is used by ganon, and would correspond to either species_genome_size.txt from the NCBI genomes FTP server or *metadata.tsv.gz from the GTDB FTP server.
The NCBI version is formatted as a 6 column tax-separated table with a header:
| Column | Column Name | Description |
|---|---|---|
| 1 | species_taxid | Taxonomic identifier of each species |
| 2 | min_ungapped_length | Minimum expected ungapped genome size of an assembly for the species |
| 3 | max_ungapped_length | Maximum expected ungapped genome size of an assembly for the species |
| 4 | expected_ungapped_length | Median genome assembly size of assemblies for the species |
| 5 | number of genomes | Number of genomes used to calculate the expected size range |
| 6 | method_determined | The method that was used to determine the size range. |
Descriptions from README_species_genome_size.txt
Example:
#species_taxid min_ungapped_length max_ungapped_length expected_ungapped_length number_of_genomes method_determined
7 4521000 6782000 5636513 5 automatic
9 281000 845000 568059 141 automatic
23 3680000 5522000 4636991 8 automatic
24 3508000 5264000 4386237 15 automatic
33 8643000 12965000 10772519 5 automatic
34 7410000 11116000 9267256 22 automatic
43 9852000 14780000 12282374 5 automaticmalt mapDB
A custom taxonomy database file from the MEGAN6 toolkit ending with .db.
This file must be unzipped before use, and is an SQLlite database consisting of two tables
info- Three column table:
id.info_string,size - Two rows:
general,Taxonomy - The
info_stringofgeneralhas a string of Created- - : : , and a size of the number of taxonomic entries in the database - The
info_stringofTaxonomyhas a string ofSource: nucl_gb.accession2taxid.gzand a size of taxonomic entries in the database
- Three column table:
mappings- A two column table:
Accession,Taxonomy - The
Accessioncolumn contains the accession ID of the sequence with version (e.g.NC_012920.1)
- A two column table:
I want to supply a custom seqid2taxid file to Kraken2
While not officially supported by Kraken2, you can speed up the Kraken2 build process by providing the pipeline a premade seqid2taxid.map file.
This file should be a tab-separated file with two columns:
- the sequence ID as represented by the first part of each
>entry of a FASTA file - the taxon ID
To supply this to the pipeline, you can give this to the --nucl2taxid parameter, as the Kraken2 seqid2taxid.map file is the same as Centrifuge’s --conversion-table file.