SRA Toolkit Documentation

Tool: abi-dump

Usage:

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

abi-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:
-F	\|	--origfmt	Excludes SRR accession on defline (read id).
Filtering:
		--spot-groups <[list]>	Filter by spot group (read group): name[,...].
-N	\|	--minSpotId <rowid>	Minimum spot id.
-X	\|	--maxSpotId <rowid>	Maximum spot id.
-R	\|	--read-filter <[filter]>	Split into files by filter value: pass\|reject\|criteria\|redacted.
-B	\|	--noDotReads	Do not output reads consisting mostly of dots.
-W	\|	--noclip	Do not clip quality left and right for spot.
Workflow and piping:
-G	\|	--spot-group	Split into files by spot group (read group).
-K	\|	--keep-empty-files	Do not delete empty files.
-O	\|	--outdir <path>	Output directory, default is working directory ('.').
-T	\|	--group-in-dirs	Split into subdirectories instead of files.
-Z	\|	--stdout	Output to stdout, all split data become joined into single stream.
		--gzip	Compress output using gzip.
		--bzip2	Compress output using bzip2.

Use examples:

abi-dump -Z -X 5 -F SRR390728

Prints the first 5 spots ("-X 5") to standard out ("-Z") with the original formatting for reads ("-F").

Possible errors and their solution:


                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.


                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.