CSV format and limits

CSV imports check the spreadsheet structure before preparing jobs. Use the column reference for input and setting values, and the rules below for file formatting and size.

File formatting

Save as UTF-8 CSV or TSV. Comma, semicolon and tab separators are supported. Quote cells containing separators or line breaks, and double any quote characters inside them. For example, a molecular modification array becomes this CSV cell:

csv

"[{""position"":2,""ccd"":""MSE""}]"

Headers must be nonempty and unique. Every row needs the same number of cells, including separators for empty final cells. Completely empty lines are ignored. A UTF-8 BOM, Windows line endings and quoted multiline FASTA content are accepted.

Import issues

Resolve errors before submitting. Use Download all … issues to retrieve the complete list:

Unknown column: Map it to an accepted column or choose Ignore. Each target can be mapped only once.
Missing or ambiguous file: Add it to the matching input and use unique, exact filenames. MSA references also need unambiguous names.
Unexpected job count: Check the combination mode, particularly its treatment of empty cells.
Invalid row or setting: Fix the reported input, format, value or tool constraint. Invalid rows are not silently skipped.
Repeated names or inputs: Duplicates are retained as separate paid jobs, with a warning.

Size limits

Imports support up to 250 data rows, 250 generated jobs, 2,048 columns and a 5 MB CSV. The prepared run has a 10 MB input-data budget; repeated large files can consume it quickly.

Complex layouts and many different setting combinations can reach the run's configuration limits before the row limit. Split the batch or reduce distinct settings when that happens. Individual tool and plan limits still apply. Native Excel workbooks, ZIP import and remote URL references are not supported by the CSV importer.

File formatting

csv

"[{""position"":2,""ccd"":""MSE""}]"

Import issues

Resolve errors before submitting. Use Download all … issues to retrieve the complete list:

Unknown column: Map it to an accepted column or choose Ignore. Each target can be mapped only once.

Missing or ambiguous file: Add it to the matching input and use unique, exact filenames. MSA references also need unambiguous names.

Unexpected job count: Check the combination mode, particularly its treatment of empty cells.

Invalid row or setting: Fix the reported input, format, value or tool constraint. Invalid rows are not silently skipped.

Repeated names or inputs: Duplicates are retained as separate paid jobs, with a warning.

Size limits

Imports support up to 250 data rows, 250 generated jobs, 2,048 columns and a 5 MB CSV. The prepared run has a 10 MB input-data budget; repeated large files can consume it quickly.