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Velvet Error: 'Could Not Write Into File'

Hi I just got Velvet up and running and I'm getting the error 'velveth: Could not write into file'...it's a paired end assembly so there are two input files, I've thrown a sudo in front of the command and the program will read the first of the two files successfully but after a 'Reading FastQ file /file/number/2' it returns the error...the velvet program folder is located in /home/usr/ and the fasta files as well as the output folder are in /home/usr/Documents...any ideas? Do I need to change some permissions? Thanks!

*Thanks for the comments, my hd space was just filling up and causing the error.

velvet error
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updated by Istvan Albert Istvan Albert • written by Jared • Jared

Just 1 stupid comment: Is your partition full ? I say that cos' it happened to me alread y ...

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written by Pasta • Pasta

2 answers

  1. don't just throw sudo in front of commands that don't work, that's a sure way to end up with problems of the like you describe
  2. instead just move the data to a folder that you are guaranteed to have write access to
  3. the location of the velvet command does not matter
  4. check for empty disk space df -k .
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written by Istvan Albert Istvan Albert

In case velvet uses your temporary directory and you have no write permission: Set your environment variable to:

export TMPDIR=/path/to/tmp
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written by Fabian Bull Fabian Bull

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