SRA Toolkit Documentation

Tool: sff-dump

Usage:

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

sff-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:
-N	\|	--minSpotId <rowid>	Minimum spot id.
-X	\|	--maxSpotId <rowid>	Maximum spot id.
-G	\|	--spot-group	Split into files by spot group ("read group").
		--spot-groups <[list]>	Filter by spot group (read group): name[,...].
Filtering:
-R	\|	--read-filter <[filter]>	Split into files by value. Values:pass\|reject\|criteria\|redacted.
Workflow and piping:
-O	\|	--outdir <path>	Output directory, default is working directory ('.').
-Z	\|	--stdout	Output to stdout, all split data become joined into single stream. Note that this is the BINARY output, does not stream sff.txt. Useful for piping to another program.
-T	\|	--group-in-dirs	Split into subdirectories instead of files.
-K	\|	--keep-empty-files	Do not delete empty files.

Use examples:

sff-dump -X 100 SRR996643

Produces a small sff file from the first 100 reads (-X 100). This is useful for verifying the formatting options before dumping a whole data file.

sff-dump -Z SRR996643 | sffinfo - | less

Allows you to view the data in sff.txt (human readable) format. With the 454 utility 'sffinfo' installed, this command dumps sff to stdout (-Z), pipes it to sffinfo ("-" needed for sffinfo to accept from stdin), and then to 'less' for viewing.

Possible errors and their solution:


                item not found while constructing within virtual database module - the path '<path>/SRR*.sra' 
                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.


                This run cannot be transformed into SFF format. Conversion cannot be completed because the source 
                lacks one or more of the data series required by the SFF format. You should be able to dump it as 
                FASTQ by running fastq-dump.

The data were not submitted as sff, thus we lack the information required to convert to sff. It is recommended that you dump into another format (fastq, sam, etc.).


                …failed with curl-error 'CURLE_COULDNT_RESOLVE_HOST'…

The toolkit is attempting to contact or download data from NCBI, but is unable to connect. Please confirm that your computer or server has Internet connectivity