Bulk download w prefetch but unable to ‘zip’ (plus more…)

Hi (beginner here so go easy on me). I’m practicing different ways of downloading. I have various questions despite doing a lot of googling on the matter.

1)

I’m trying to run something like this (I know these aren’t the exact commands for prefetch):

prefetch $(<SRAacclist.txt) --gzip --outdir /scratch/eg5/trial2/sns/fqdata

When I run prefetch $(<SRAacclist.txt) my files do get downloaded of course, but they’re not zipped, or in the folder I want them to be. Additionally it downloads extra sra folders, when all I want is the fastq file. How can I specify this?

2)
All my modules are loaded ( edirect, sra etc) yet I keep getting a not found error for ” –format”

esearch -db sra -query PRJNA386935 | efetch -format runinfo | cut -d "," -f 1 > SRR.numbers

Any ideas?

3)
For downloading from SRA to hpc cluster folder:
prefetch vs parallel vs wget vs fastqdump . What do you guys think? So far prefetch jas been the fastest, but fastq dump seems to be most easily ‘customizable’ .