Trying this code

sr320$ ./fastq-dump -A SR327417 /Volumes/Bay3/OysterGenomeBGI/SRX089200/SRR327417/SRR327417.sra -O /Volumes/Bay4\ scratch/BGIfosmids


Also comparing BGIresequencing import difference in CLC4.0 and 4.8







NOTE that different OS bit systems have different versions of the softwares with different options.

On greenbird: 
Version: 2.1.0

robertsmac:sratoolkit.2.1.0-mac64 sr320$ ./fastq-dump --help

Usage:
  ./fastq-dump [options] [ -A ] <accession>
  ./fastq-dump [options] <path>

  -A, --accession                      Accession.

Options:

  -O, --outdir                         Output directory. Default: '.'
  -N, --minSpotId                      Minimum spot id to output.
  -X, --maxSpotId                      Maximum spot id to output.
  -G, --spot-group                     Split into files by SPOT_GROUP (member name).
  -GL, --spot-group-list [<list>]       Filter by SPOT_GROUP (member): name[,...].
  -R, --read-filter [<filter>]         Split into files by READ_FILTER value,
                         optional filter by a value: pass|reject|criteria|redacted.
  -T, --group-in-dirs                  Split into subdirectories instead of files.
  -K, --keep-empty-files               Do not delete empty files.
  -L, --log-level <level>              Logging level: fatal|sys|int|err|warn|info. Default: warn
  -H, --help                           Prints this message.

Format options:

  -M, --minReadLen <len>               Filter by minimum read length.
  -E, --qual-filter                    Filter by quality.
  -TR, --skip-technical                 Filter technical reads.
  -W, --clip                           Clip quality left and right for spot

NOTE: above 4 options were changed, to restore behaviour run with: -M 25 -E -TR -W

  -F, --origfmt                        Excludes SRR accession & length on defline.
  -C, --dumpcs [cskey]                 Dump color space sequence (default for ABI SOLID), single letter color space key is optional.
  -B, --dumpbase                       Dump base sequence (default for other than ABI SOLID).
  -Q, --offset                         Offset to use for quality conversion. Default: 33
  -I, --readids                        Append read id after spot id as 'accession.spot.readid' on defline.
  -SF, --complete                       Dump reads in a single file.
  -SL, --one-line                       Join reads on a single line.
  -DB, --defline-seq                    sequence defline format specification. String of characters and/or variables.

          Variables are one of:
            $ac - accession, $si - spot id, $sn - spot name, $sg - spot group (barcode),
            $sl - spot length in bases, $ri - read number, $rn - read name, $rl - read length in bases.
          '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed.
          Empty value is empty string or 0 for numeric variables.
          Ex: @$sn[_$rn]/$ri - '_$rn' is omitted if name is empty

  -DQ, --defline-qual                   quailty defline format specification. If -DB is provided but -DQ ommitted, -DB value is used.
  -HS, --helicos                        Helicos style.
  -FA, --fasta                          Fasta only, no qualities.

Version: 2.1.0