As @terdon said, it is better to use fasterq-dump, and the command:
fasterq-dump --option-file SraAccList.txt doesn't work. When I try it, I just get the usage message:
$ fasterq-dump --option-file SraAccList.txt
Usage:
fasterq-dump <path> [options]
fasterq-dump <accession> [options]
Options:
-F|--format format (special, fastq, default=fastq)
-o|--outfile output-file
-O|--outdir output-dir
-b|--bufsize size of file-buffer dflt=1MB
-c|--curcache size of cursor-cache dflt=10MB
-m|--mem memory limit for sorting dflt=100MB
-t|--temp where to put temp. files dflt=curr dir
-e|--threads how many thread dflt=6
-p|--progress show progress
-x|--details print details
-s|--split-spot split spots into reads
-S|--split-files write reads into different files
-3|--split-3 writes single reads in special file
--concatenate-reads writes whole spots into one file
-Z|--stdout print output to stdout
-f|--force force to overwrite existing file(s)
--skip-technical skip technical reads
--include-technical include technical reads
-M|--min-read-len filter by sequence-len
--table which seq-table to use in case of pacbio
-B|--bases filter by bases
-A|--append append to output-file
--fasta produce FASTA output
--fasta-unsorted produce FASTA output, unsorted
--fasta-ref-tbl produce FASTA output from REFERENCE tbl
--fasta-concat-all concatenate all rows and produce FASTA
--internal-ref extract only internal REFERENCEs
--external-ref extract only external REFERENCEs
--ref-name extract only these REFERENCEs
--ref-report enumerate references
--use-name print name instead of seq-id
--seq-defline custom defline for sequence: $ac=accession,
$sn=spot-name, $sg=spot-group, $si=spot-id,
$ri=read-id, $rl=read-length
--qual-defline custom defline for qualities: same as
seq-defline
-U|--only-unaligned process only unaligned reads
-a|--only-aligned process only aligned reads
--disk-limit explicitly set disk-limit
--disk-limit-tmp explicitly set disk-limit for temp. files
--size-check switch to control: on=perform size-check
(default), off=do not perform size-check,
only=perform size-check only
--ngc <PATH> PATH to ngc file
-h|--help Output brief explanation for the program.
-V|--version Display the version of the program then
quit.
-L|--log-level <level> Logging level as number or enum string. One
of (fatal|sys|int|err|warn|info|debug) or
(0-6) Current/default is warn.
-v|--verbose Increase the verbosity of the program
status messages. Use multiple times for more
verbosity. Negates quiet.
-q|--quiet Turn off all status messages for the
program. Negated by verbose.
--option-file <file> Read more options and parameters from the
file.
for more information visit:
https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump
fasterq-dump : 3.0.6
