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fastq-dump not working in loop

I am running loop to download fastq files through fastq-dump but it gives following error

fastq-dump.3.1.1 err: error unexpected while resolving query within virtual file system module - No accession to process ( 500 )
Failed to call external services.

Note. fastq-dump is working fine for single accession.

fastq-dump
• 1,928 views • link
updated by Ram Ram • written by Bushra Bibi Bushra Bibi

Can you add a snippet of your code?

Based on the error it seems you are not providing an accession number.

Regards,

Nitin N.

• 0 views • link
written by Nitin Narwade Nitin Narwade 
input=/home/data/Downloads/acc.txt
for file in $(cat $input)
do 
    fastq-dump --orig-fmt --gzip $file -O /home/data/Downloads/raw/
done
• 0 views • link
written by Bushra Bibi Bushra Bibi

If I am not wrong the accession number is a positional argument in fastq-dump, so probably your command should be something like this,

fastq-dump $file --orig-fmt --gzip -O /home/data/Downloads/raw/

If this doesn't work, it could be a problem with newline character in the accession number, try removing it in this case.

Just asking out of curiosity did you try running your command without a loop? I mean using a single static accession number.

Regards,

Nitin N.

• 0 views • link
written by Nitin Narwade Nitin Narwade

Yes I tried using a single accession and and it worked

• 0 views • link
written by Bushra Bibi Bushra Bibi

show the code you ran?

• 0 views • link
written by 1769mkc 1769mkc

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