Issues downloading fastq data
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8 days ago

Hello,

I am experiencing issues when downloading from SRA several data using the following command, and I do not understand how to manage it.......

# in ids_mod1.txt file there are 3 SRR ids and I am using WSL ubuntu.

$ cat ids_mod1.txt | parallel fastq-dump --split-files {}

2021-04-07T18:10:26 fastq-dump.2.10.9 err: error unexpected while resolving query within virtual file system module - No accession to process ( 500 )
Failed to call external services.
2021-04-07T18:10:26 fastq-dump.2.10.9 err: error unexpected while resolving query within virtual file system module - No accession to process ( 500 )
Failed to call external services.

I find similar problems using GUI parallel with other commands so I though the issue was with parallel but if I use parallel with echo... parallel do its work.....

Could somebody give me a hand with this.... many thanks in advance

fastq-dump parallel SRA • 123 views
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I just used basically the same command (with a different input list of accession numbers) and it worked without issue. I would double check ids_mod1.txt to look for formatting errors.

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many thanks Dave, unfortunately no formatting errors :-(

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