Question: Velvet Error: 'Could Not Write Into File'
0
gravatar for Jared
8.2 years ago by
Jared10
Jared10 wrote:

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 • 3.1k views
ADD COMMENTlink modified 8.2 years ago by Istvan Albert ♦♦ 81k • written 8.2 years ago by Jared10

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

ADD REPLYlink written 8.2 years ago by Pasta1.3k
3
gravatar for Istvan Albert
8.2 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:
  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 .
ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Istvan Albert ♦♦ 81k
0
gravatar for Fabian Bull
8.2 years ago by
Fabian Bull1.3k
German
Fabian Bull1.3k wrote:

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

export TMPDIR=/path/to/tmp
ADD COMMENTlink written 8.2 years ago by Fabian Bull1.3k
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