Carts and Workspace

Carts versus Workspace Sets

Carts and Workspace Sets store existing data in IMG!
They cannot be used to upload private genomes or genes that are NOT in IMG.
See IMG Submission to upload my private genome.

Carts

Carts are available in both IMG/M and IMG/MER. Carts are used to quickly save items of interest (Genomes, Genes, Scaffolds, Functions).
The data in carts is NOT saved in public IMG/M.
IMG/MER carts are persistent between log ins and log outs.
Tip: It is best to save your carts into a Workspaces Set for long term storage.

Please see Analysis Carts Documents

Workspace

Workspace is ONLY available in IMG/MER (requires a JGI SSO account).
Workspace Sets are analogous to 4 major types of carts:
Genome Set, Gene Set, Scaffold Set, and Function Set.
All your workspace sets are private.

Please see Workspace Help Document

Workspace Jobs

IMG has limited resources. User workspace has a disk space limit of 5 GB per user.

The workspace is not a tool to bulk download my data sets!
Workspace is a background computation analysis tool and it should NOT be used to get ALL functional annotations for my Genome Set or my private data sets uploaded via IMG Submission
All the functional annotations for your private data set are included in the IMG download bundle, available at JGI's Data Portal site.

See JGI Data Portal for bulk downloads.
See IMG Webinar IMG data export and download

Please see Workspace Help Document

My Job is still Running

Job times can vary greatly from a few hours to many days.
It is better to submit many smaller jobs than one big job.

Tips on making jobs faster:

Create smaller batch jobs not one big job. Big jobs require more resources and a lot more time to complete.
Create a Blast job with one sequence against a few genomes instead of many sequences against a lot of genomes. The latter requires more resources and will take days to complete.
Group function families into one set, do not mix functions.

Please see Workspace Help Document

Cart Import File Format

The formats for carts are all similar. A text file where the first line is the column name followed by an id on a newline. One id per newline.

Genome Cart

A text file with one column: a header taxon_oid and a list of IMG genome ids.
For example:

taxon_oid

2728369338

2660238774

Scaffold Cart

A text file with one column: a header Scaffold ID and a list of IMG scaffold ids.
There are 2 formats of scaffold ids in IMG.

Scaffolds from isolate genomes. These are unique numeric ids, eg. 2728434447
Scaffolds from metagenomes. These scaffold ids are more complex and has a string format of; [IMG taxon id] [assembled] [IMG scaffold id|original id]. There is just ONE space between identifiers.

Scaffold ID

2728434447

2728434448

2728434449

3300024970 assembled Ga0207967_1000001

3300024970 assembled Ga0207967_1000004

3300001986 assembled scaffold00009

3300045982 assembled NODE_325_length_112208_cov_14.572156

3300037602 assembled scaffold_4_c2

Gene Cart

A text file with one column: a header gene_oid and a list of IMG gene ids.

gene_oid

2730052999

3300024970 assembled Ga0207967_1000001502

Function Cart

A text file with one column: a header func_id and a list of function ids.

func_id

COG0002

COG0004

TIGR00002

TIGR00003

pfam00297

pfam01411

Workspace Set Import Format

Workspace Genome Set

The import file for a Genome Set is different from that for a Genome Cart.
The header format is: "genome[TAB][set_name]"
Where:

genome - a set type
[TAB] - a tab space
[set_name] - set name, do not use spaces or special characters, underscores are OK.

genome[TAB]ani_genomes_set01

2509276021

2516653047

Workspace Scaffold Set

The import file for a Scaffold Set is different from that for a Scaffold Cart.
The header format is: "scaffold[TAB][set_name]"
Where:

scaffold - a set type
[TAB] - a tab space
[set_name] - set name, do not use spaces or special characters, underscores are OK.

Isolate Id format [scaffold id]

Where:

[scaffold id] - IMG's scaffold id

Metagenome Id format separated by a space: [genome id] [assembled|unassembled] [metagenome scaffold id|original id]

Where:

[genome id] - IMG's genome id
[assembled|unassembled] - the word "assembled" or "unassembled"
[metagenome scaffold id|original id] - the metagenome's scaffold "id" or "original id"

scaffold[TAB]my_mix_scaffolds

3300001986 unassembled JGI24718J22297_300355

3300001986 unassembled JGI24718J22297_311192

644736362

3300000547 assembled PR_CR_10_Liq_2_inCRDRAFT_1000001

scaffold[TAB]scaffolds_with_original_id

3300001986 assembled scaffold00009

3300045982 assembled NODE_325_length_112208_cov_14.572156

3300037602 assembled scaffold_4_c2

Workspace Gene Set

The import file for a Gene Set is different from that for a Gene Cart.
The header format is: "gene[TAB][set_name]"
Where:

gene - a set type
[TAB] - a tab space
[set_name] - set name, do not use spaces or special characters, underscores are OK.

Isolate Id format [gene id]

Where:

[gene id] - IMG's gene id

Metagenome Id format separated by a space: [genome id] [assembled|unassembled] [metagenome gene id]

Where:

[genome id] - IMG's genome id
[assembled|unassembled] - the word "assembled" or "unassembled"
[metagenome gene id] - the metagenome's gene id

gene[TAB]mix_set

2781673466

2781673467

3300001986 assembled JGI24718J22297_10004012

3300001986 assembled JGI24718J22297_10018415

Workspace Function Set

The import file for a Function Set is different from that for a Function Cart.
The header format is: "function[TAB][set_name]"
Where:

function - a set type
[TAB] - a tab space
[set_name] - set name, do not use spaces or special characters, underscores are OK.

function[TAB]mix_set

TIGR00002

TIGR00003

pfam01411

COG0002

COG0004

pfam00297

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