SRA Toolkit Documentation

Tool: illumina-dump

Usage:

illumina-dump [options] <path/file> [<path/file> ...]

illumina-dump [options] <accession>

Frequently Used Options:

General:
-h	\|	--help	Displays ALL options, general usage, and version information.
-V	\|	--version	Display the version of the program.
Data formatting:
-A	\|	--accession <accession>	Replaces accession derived from <accession> in filename(s) and deflines.
-x	\|	--qseq <1\|2>	Output QSEQ format: whole spot (1) or split by reads (2).
Filtering:
-N	\|	--minSpotId <rowid>	Minimum spot id.
-X	\|	--maxSpotId <rowid>	Maximum spot id.
-G	\|	--spot-group	Split into files by spot group ("read group").
Workflow and piping:
-O	\|	--outdir <path>	Output directory, default is working directory ('.').
-Z	\|	--stdout	Output to stdout, all split data becomes joined into a single stream.
		--gzip	Compress output using gzip.
		--bzip2	Compress output using bzip2.

Use examples:

illumina-dump -A sample1 --qseq 2 SRR390728

Produces file with SRR# accession in filenames and deflines replaced with "sample1" (-A sample1) in qseq format with non-split spots (--qseq 2).

illumina-dump -r -O Illumina --gzip SRR390728

Produces the sequence reads only (-r), writes the output to a sub-directory "Illumina" in the CWD (-O Illumina) and gzips the file(s) (--gzip).

Possible errors and their solution:


                param incorrect while reading argument list within application support module

This error indicates a malformed command line, check your dump command for proper typos and proper usage of options.


                item not found while constructing within virtual database module - the path 'SRR*' cannot be opened as database or table

This error indicates that the .sra file cannot be found. Confirm that the path to the file is correct.