Rename files with loop variable name

Rename files with loop variable name

I am trying to download a bunch of files and rename them as I go. the download portion works correctly, but i can't get it to rename the files. This is the script I'm using:

I am trying to download a bunch of files and rename them as I go. the download portion works correctly, but i can't get it to rename the files. This is the script I'm using:

COUNTER=0
for (( i = 696; i <= 773; i++ ))
  do
  fastq-dump --split-3 --accession SRR546$i
mv SRR546"$i"_1 ./"$COUNTER"mVD_SRR546$i_1
mv SRR546"$i"_2 ./"$COUNTER"mVD_SRR546$i_2
gzip *.fastq

COUNTER=$[COUNTER + 1] done

This will correctly download the file SRR546696, SRR546697 etc. but does nothing to rename them.

I also tried using:

rename 's/SRR/"$COUNTER"mVD_SRR/' *.fastq

but this also did nothing.

linux

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