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I was able to download all of the SRA files for a specific bioproject using the command:

prefetch -O output_directory --option-file SRR_Acc_List.txt

I then tried the following command to download those SRA files into FASTQ files:

find -name \*.sra -exec bsub fastq-dump --split-3 --gzip {} \;

It gave the error:

find: illegal option -- n
usage: find [-H | -L | -P] [-EXdsx] [-f path] path ... [expression]
       find [-H | -L | -P] [-EXdsx] -f path [path ...] [expression]

I then tried to add the path:

find /Users/lucykelly/Desktop/Assel_paper/output_directory -name '*.sra' -exec bsub fastq-dump --split-3 --gzip {} \;

It gave the error:

find: bsub: No such file or directory

I then tried

find . -name '*.sra' -exec fasterq-dump --gzip {} \;

and it gave the error:

find: fasterq-dump: No such file or directory
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  • $\begingroup$ I agree with @ATPoint. At first I thought it was bsub within the Slurm cluster. If you use which fasterq-dump it should throw a blank. The bsub error is weird because you should be on the cluster right? Anyway once diagnosed its easy to solve. $\endgroup$
    – M__
    Mar 13 at 3:05

1 Answer 1

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That is a classical problem where the folder containing the binary of the tool is not in PATH, see for example https://askubuntu.com/questions/109381/how-to-add-path-of-a-program-to-path-environment-variable or many other threads towards PATH in the SE network.

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  • $\begingroup$ Thank you so much @ATpoint $\endgroup$
    – Lucy
    Mar 13 at 23:22

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