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Old 11-11-2013, 11:22 AM   #1
Kimist99
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Default Problems using wgsim in Linux/Ubuntu

Hello All!

I'm a relative newbie to Bioinformatics and I'm having problems with the code I'm using to generate reads from a reference sequence.

I'm using Linux/Ubuntu, and here is the code I'm using along with the error message:

Kimist@Kimist99:~/seqaln$ ./wgsim.c -N 10000 hg18.chr20.10k_200k.fa sim_1.fq sim_2.fq > sim.mutation.txt
./wgsim.c: line 1: /bin: Is a directory
./wgsim.c: line 3: syntax error near unexpected token `c'
./wgsim.c: line 3: ` Copyright (c) 2008 Genome Research Ltd (GRL).'


Any help you can provide is greatly appreciated, I feel like this is something easy and that I just don't have the expertise to figure it out. My classmates all use Macs.
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Old 11-11-2013, 11:28 AM   #2
lindenb
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wgsim is a C program. If it hasn't been done, you need to compile it with MAKE it before using it.
the command will be:


/path/to/wgsim -N 10000 hg18.chr20.10k_200k.fa sim_1.fq sim_2.fq > sim.mutation.txt
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Old 11-11-2013, 11:38 AM   #3
Kimist99
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Quote:
Originally Posted by lindenb View Post
wgsim is a C program. If it hasn't been done, you need to compile it with MAKE it before using it.
the command will be:


/path/to/wgsim -N 10000 hg18.chr20.10k_200k.fa sim_1.fq sim_2.fq > sim.mutation.txt
Thanks for the quick repsonse!

I thought I did compile it with MAKE, but apparently I didn't.

How can I confirm the compiling was done?

Thanks again!
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Old 11-11-2013, 11:50 AM   #4
dnafp
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At the command prompt type:
file /path/to/wgsim
this should return you something like "elf executable" ...

If you can open that file in an editor, it's usually not compiled yet. You'll likely need to find the execuable wgsim without the ending ".c".
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Old 11-11-2013, 11:51 AM   #5
lindenb
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go in the wgsim.c folder (samtools/misc) and type "make" or "make wgsim"
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Old 11-11-2013, 12:06 PM   #6
Kimist99
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Quote:
Originally Posted by lindenb View Post
go in the wgsim.c folder (samtools/misc) and type "make" or "make wgsim"
Now I'm getting the following error:

:~/seqaln$ make wgsim
gcc -g -Wall -O2 wgsim.c -o wgsim
wgsim.c:39:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^
compilation terminated.
make: *** [wgsim] Error 1

Thanks again for the advice!
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Old 11-11-2013, 12:19 PM   #7
lindenb
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install zlib and zlib-devel packages :

sudo apt-get install zlib-devel
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Old 11-11-2013, 01:50 PM   #8
Kimist99
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Quote:
Originally Posted by lindenb View Post
install zlib and zlib-devel packages :

sudo apt-get install zlib-devel
After a couple hours of trying to trouble shoot this myself, I get nothing but the following message:

~/seqaln$ sudo apt-get install zlib-devel
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package zlib-devel

I assumed the package was part of Samtools-0.1.19.
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Old 11-11-2013, 03:42 PM   #9
GenoMax
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Package you need to install is called "zlib1g-dev". Package page: http://packages.ubuntu.com/lucid/libdevel/zlib1g-dev

If you are new to ubuntu doing the installs through the "package/software manager" is probably a better idea.
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Old 11-11-2013, 04:14 PM   #10
Kimist99
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Quote:
Originally Posted by GenoMax View Post
Package you need to install is called "zlib1g-dev". Package page: http://packages.ubuntu.com/lucid/libdevel/zlib1g-dev

If you are new to ubuntu doing the installs through the "package/software manager" is probably a better idea.
Worked like a charm, thanks again!
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Old 11-11-2013, 04:37 PM   #11
Kimist99
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Bottom line for folks using samtools in Ubuntu, you need to make sure you download all the necessary packages before trying to run it.
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Old 11-11-2013, 05:56 PM   #12
eco32i
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The easiest way to use samtools on ubuntu is just to install the package via apt-get:

Code:
$ sudo apt-get install samtools
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Old 11-11-2013, 06:30 PM   #13
Kimist99
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Quote:
Originally Posted by eco32i View Post
The easiest way to use samtools on ubuntu is just to install the package via apt-get:

Code:
$ sudo apt-get install samtools
Unforntuantely, doing that didn't work until after I donwloaded the packages mentioned above.
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