SOAP denovo permission denied

Question

[minesrebollo]

Hi! I'm new to bioinformatics and linux. I've downloaded the latest pre-compiled binary version of SOAPdenovo2 and placed it in a directory in my Desktop. I unpacked it using tar -zxf. I also created a config file and have all my fastq, fasta and bam files ready on another directory in my Desktop.

My issue is that when I change directory to /bin to execute (i supposed i have to go there to execute it) and type the command:

/path/SOAPdenovo-63mer all -s /path/config_file -K 63 -R -o graph_prefix 1>ass.log 2>ass.err

I get Bash: ass.log permission denied

I already tried chmod 777 to SOAPdenovo-63mer and to ass.log so that they have all the permissions and even added from /etc with sudo nano /etc/sudoers the user to execute with admin permission eve though there's only one user and is the admin.

What should I do? Thanks!!

[5heikki]

 1>ass.log 2>ass.err

You don't want to write these files to your /bin, direct them to some sensible place like /home/username/experimentname/

[minesrebollo]

Thanks 5heikki for your answer!

I did what you said and solved that but right after came across with another problem which I describe below. I've been reading more about UNIX but still can't realize what im doing wrong.

I'd really appreciate your help :)

[WouterDeCoster]

Hello minesrebollo!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=201272

This is typically not recommended as it runs the risk of annoying people in both communities.

[minesrebollo]

Sorry, I am new to all this. Thanks for the advice, wont do it again.

Answer 1

[WouterDeCoster]

You don't have to be in /bin to execute it, assuming /bin is in your $PATH. So that means you can execute it from anywhere.

You get this error because you have no writing permission to /bin You requested the log file (and err file) to be made in /bin and your user has no permission to do so. Instead, execute the script somewhere else and/or point the location of the files to a directory to which you can write.

[minesrebollo]

Hi WouterDeCoster, thanks a lot for your answer.

I executed the script from the directory where SOAPdenovo-63mer is which I can write and I still cant do it. Fist I tried: ./SOAPdenovo-63mer all -s /path/config_file -K 63 -R -o graph_prefix 1>ass.log 2>ass.err and in ass.err I get: bash: ./SOAPdenovo-63mer: binary file cannot be executed so I executed the same but with sudo first. Now in ass.err I get: ./SOAPdenovo-63mer: 4: ./SOAPdenovo-63mer: Syntax error: "(" unexpected

Any idea how to solve it?

Thanks again!

[WouterDeCoster]

It's not good practice to use sudo to run tools like this, that's only for installing software or performing crucial administrative tasks on your system. I expect SOAPdenovo to be safe, but when you run unknown software with sudo you give it all power on your system to modify/delete whatever it wants to. You are giving full access to everything. That might give nasty results.

Did you install SOAPdenovo yourself?

[minesrebollo]

I downloaded the pre-compiled version that is supposed to be ready to be executed directly. Should I install it?

[WouterDeCoster]

Which operating system do you use? You could try installing it as described on the GitHub page. Based on that page, Soapdenovo has been replaced by megahit.