Velvet Error: 'Could Not Write Into File'

Question

[Jared]

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.

[Pasta]

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

Answer 1

[Istvan Albert]

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 .

Answer 2

[Fabian Bull]

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

export TMPDIR=/path/to/tmp