Try this one. When you didn't remove SRA files, you can use the following:

for i in `ls *.gz`; 
do 
  SRR=${i%%_*}; 
  echo $SRR >> list.txt; 
done

for j in `sort -u list.txt`
do
  vdb-validate $j
done

if you have already removed SRA and only kept fastq, and suppose your fastq is from this way:

fastq-dump --split-files --gzip SRR949210

Then you can try:

for i in `ls *fastq.gz`; 
do 
gunzip -t $i 2 > $i.err
done
find . -name "*err" -type f -size +0c -exec -larth {} \;

vdb-validate operates on the SRA archive. if you are streaming fastq from SRA using local toolkit install, you'll get an error if the process is interrupted. otherwise your output will be complete. you can verify by checking your output stats against the stats stored in SRA using sra-stat -x (use --statistics to get deeper detail including at readgroup level and quality score distribution). or check individually by looking at SRA RunBrowser which displays basic stats.

Md5sum value get generated using following command:

md5sum *.fastq.gz >md5sum.txt

md5sum.txt will contain file name and corresponding md5sum value

Note: Run this command on linux command line, at file location only.