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**shashankgupta** · 02-04-2015, 02:15 AM

indeed. i used the above command.

when i tried to use AUGUSTUS, i got an error

[root@root augustus.2.5.5]# augustus --species=SPECIES 454AllContigs.fna > output.gff
bash: augustus: command not found

**sarvidsson** · 02-04-2015, 02:22 AM

Originally posted by shashankgupta View Post

indeed. i used the above command.

when i tried to use AUGUSTUS, i got an error

[root@root augustus.2.5.5]# augustus --species=SPECIES 454AllContigs.fna > output.gff
bash: augustus: command not found

This means that the executable "augustus" wasn't found. Did you perform all steps in the tutorial, without getting error messages? Especially the "make" and "make install" (as you seem to be logged in as root, you should be able to do that) commands are very, very important and need to finish without errors.

**sarvidsson** · 02-04-2015, 02:25 AM

Originally posted by shashankgupta View Post

indeed. i used the above command.

when i tried to use AUGUSTUS, i got an error

[root@root augustus.2.5.5]# augustus --species=SPECIES 454AllContigs.fna > output.gff
bash: augustus: command not found

Also, you need to replace "SPECIES" with one of the choices of trained species listed in the Augustus documentation.

**shashankgupta** · 02-04-2015, 02:29 AM

[root@root augustus.2.5.5]# cd src/
[root@root src]# make
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o genbank.o genbank.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o properties.o properties.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o pp_profile.o pp_profile.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o pp_hitseq.o pp_hitseq.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o pp_scoring.o pp_scoring.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o statemodel.o statemodel.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o namgene.o namgene.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o types.o types.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o gene.o gene.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o evaluation.o evaluation.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o motif.o motif.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o geneticcode.o geneticcode.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o hints.o hints.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o extrinsicinfo.o extrinsicinfo.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o projectio.o projectio.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o intronmodel.o intronmodel.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o exonmodel.o exonmodel.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o igenicmodel.o igenicmodel.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o utrmodel.o utrmodel.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o merkmal.o merkmal.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o vitmatrix.o vitmatrix.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o lldouble.o lldouble.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o commontrain.o commontrain.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o igenictrain.o igenictrain.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o introntrain.o introntrain.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o exontrain.o exontrain.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o utrtrain.o utrtrain.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o dummy.o dummy.cc -I../include -I.
g++ -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o dummy.o -I../include -I.
/usr/bin/ld: cannot find -lm
collect2: ld returned 1 exit status
make: *** [augustus] Error 1

1 error i got

**shashankgupta** · 02-04-2015, 02:30 AM

Originally posted by sarvidsson View Post

This means that the executable "augustus" wasn't found. Did you perform all steps in the tutorial, without getting error messages? Especially the "make" and "make install" (as you seem to be logged in as root, you should be able to do that) commands are very, very important and need to finish without errors.

[root@root augustus.2.5.5]# cd src/
[root@root src]# make
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o genbank.o genbank.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o properties.o properties.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o pp_profile.o pp_profile.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o pp_hitseq.o pp_hitseq.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o pp_scoring.o pp_scoring.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o statemodel.o statemodel.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o namgene.o namgene.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o types.o types.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o gene.o gene.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o evaluation.o evaluation.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o motif.o motif.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o geneticcode.o geneticcode.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o hints.o hints.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o extrinsicinfo.o extrinsicinfo.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o projectio.o projectio.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o intronmodel.o intronmodel.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o exonmodel.o exonmodel.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o igenicmodel.o igenicmodel.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o utrmodel.o utrmodel.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o merkmal.o merkmal.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o vitmatrix.o vitmatrix.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o lldouble.o lldouble.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o commontrain.o commontrain.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o igenictrain.o igenictrain.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o introntrain.o introntrain.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o exontrain.o exontrain.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o utrtrain.o utrtrain.cc -I../include -I.
g++ -c -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o dummy.o dummy.cc -I../include -I.
g++ -Wall -Wno-sign-compare -ansi -pedantic -O2 -static -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o dummy.o -I../include -I.
/usr/bin/ld: cannot find -lm
collect2: ld returned 1 exit status
make: *** [augustus] Error 1

i got 1 error

**shashankgupta** · 02-04-2015, 09:22 PM

i tried in other system, and make command works perfectly fine....

$PWD
/home/qiime/Desktop/augustus.2.5.5/config/

and then

export AUGUSTUS_CONFIG_PATH=/home/qiime/Desktop/augustus.2.5.5/config/

then

AUGUSTUS --species=HOMO sapiens 454AllContigs.fna > output.gff

and again the same error
AUGUSTUS : command not found

Anuy suggestion ?

**sarvidsson** · 02-05-2015, 02:38 AM

Originally posted by shashankgupta View Post

i tried in other system, and make command works perfectly fine....
...
AUGUSTUS --species=HOMO sapiens 454AllContigs.fna > output.gff

and again the same error
AUGUSTUS : command not found

...

Try

Code:

augustus --species="Homo sapiens" 454AllContigs.fna > output.gff

On UNIX-like systems (e.g. Linux), filename case is crucial. Also, arguments containing spaces should be enclosed by quotes to be interpreted as one argument.

If the "make install" worked properly as you stated on this other system, the command

Code:

which augustus

should print something like

Code:

/usr/local/bin/augustus

If you get no output from that command, something didn't work...

**shashankgupta** · 02-05-2015, 02:54 AM

i undrstand the concept about the case sensitivity.
when i used command

which augustus

no output from the command

i tried everything to make it install, please walk with me to install it.

**GenoMax** · 02-05-2015, 04:01 AM

Can you post the output of this command?

Code:

$ ls -lRh /root/Desktop/augustus.2.5.5

We need to figure out first if you have manged to compile augustus/have the binary available.

**sarvidsson** · 02-05-2015, 04:31 AM

Also realized they do provide binaries. Why didn't you get the latest version (3.0.3)?

This worked for me on a pretty much stock Ubuntu 14.04 machine:

Code:

cd /illumina/software
wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.0.3.tar.gz
tar -xzvf augustus-3.0.3.tar.gz
export AUGUSTUS_CONFIG_PATH=/illumina/software/augustus-3.0.3/config/
export PATH=$PATH:/illumina/software/augustus-3.0.3/bin:/illumina/software/augustus-3.0.3/scripts/
cd augustus-3.0.3
augustus --species=human --UTR=on examples/example.fa

Just replace "/illumina/software" for wherever you'd like to install it, and try that out...

**shashankgupta** · 02-05-2015, 07:15 AM

i give it a try for latest version (3.0.3) in ubuntu

**GenoMax** · 02-05-2015, 07:19 AM

So is it working now? Or you will try this later.

**shashankgupta** · 02-05-2015, 07:26 AM

miracle

it works pretty good.. tooks hardly 20 min. . Thanks !
I appreciate it.
Best !
Shashank

**shashankgupta** · 02-05-2015, 07:52 AM

Hi, as you helped me to install AUGUSTUS, can you tell me as well how can i install MAKER (genome annotation tool) as well.

I really need to do this.

**sarvidsson** · 02-05-2015, 07:56 AM

I'm a commercial user, so I'd need a license to download it. Maybe someone from academia can help you.

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