SOAP denovo permission denied

mines · 11-22-2016, 06:10 PM

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 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 evethough there's only one user and is the admin.

What should I do?
Thanks!!

GenoMax · 11-22-2016, 06:44 PM

You don't want to write data files to the SOAPdenovo/bin directory. You can add a path to /some_path/ass.log and /some_path/ass.err files so they are saved somewhere else other than the SOAP dir hierarchy.

mines · 11-22-2016, 06:53 PM

Hi GenoMax, thanks a lot for your answer.

I don't have any SOAPdenovo directory in /bin, i just go there to execute it, should I do something about that?

The ass.log and ass.err files are automatically created in the SOAPdenovo directory in my desktop where I have the SOAPdenovo-63mer file.
The ass.err file says SOAPdenovo-63mer command not found.

Thanks again!

mines · 11-22-2016, 06:58 PM

Sorry, I meant bam files instead of bin when I wrote fastq, fasta and bin files ready.

GenoMax · 11-23-2016, 04:03 AM

You don't need to go to /bin directory to execute other programs (e.g. SOAP). You may want to spend a bit of time understanding basics of UNIX to clarify this. Follow this guide.

mines · 11-27-2016, 11:19 AM

I definitely will. Thanks for the guide GenoMax!

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11-22-2016, 06:10 PM	#1
mines Junior Member Location: Uruguay Join Date: Nov 2016 Posts: 4	SOAP denovo permission denied 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 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 evethough there's only one user and is the admin. What should I do? Thanks!! Last edited by mines; 11-22-2016 at 06:57 PM.

11-22-2016, 06:44 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	You don't want to write data files to the SOAPdenovo/bin directory. You can add a path to /some_path/ass.log and /some_path/ass.err files so they are saved somewhere else other than the SOAP dir hierarchy.

11-22-2016, 06:53 PM	#3
mines Junior Member Location: Uruguay Join Date: Nov 2016 Posts: 4	Hi GenoMax, thanks a lot for your answer. I don't have any SOAPdenovo directory in /bin, i just go there to execute it, should I do something about that? The ass.log and ass.err files are automatically created in the SOAPdenovo directory in my desktop where I have the SOAPdenovo-63mer file. The ass.err file says SOAPdenovo-63mer command not found. Thanks again!

11-22-2016, 06:58 PM	#4
mines Junior Member Location: Uruguay Join Date: Nov 2016 Posts: 4	Sorry, I meant bam files instead of bin when I wrote fastq, fasta and bin files ready.

11-23-2016, 04:03 AM	#5
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	You don't need to go to /bin directory to execute other programs (e.g. SOAP). You may want to spend a bit of time understanding basics of UNIX to clarify this. Follow this guide.

11-27-2016, 11:19 AM	#6
mines Junior Member Location: Uruguay Join Date: Nov 2016 Posts: 4	I definitely will. Thanks for the guide GenoMax!