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SRA Toolkit Documentation

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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.