Question: Augustus Installation error
0
gravatar for ashaneev07
4 months ago by
ashaneev0710
ashaneev0710 wrote:

Hiii.... i'm facing installation issue with augustus on my ubuntu (14.04). I have installed bamtools manually for this but, showing the following error.. Thanks.

sudo make
mkdir -p bin
cd src && make
make[1]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/src'
echo "-Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 " > cxxflags
make[1]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/src'
cd auxprogs && make
make[1]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs'
cd bam2hints; make;
make[2]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/bam2hints'
make[2]: `bam2hints' is up to date.
make[2]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[2]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/compileSpliceCands'
make[2]: `compileSpliceCands' is up to date.
make[2]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/compileSpliceCands'
cd filterBam; make;
make[2]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam/src'
g++     -std=c++0x  -c filterBam.cc -o filterBam.o -I=/home/dcb/Documents/EV/Maker/bamtools/include/bamtools -Iheaders -I./bamtools
filterBam.cc:14:31: fatal error: api/BamReader.h: No such file or directory
 #include <api/BamReader.h>    
                               ^
compilation terminated.
make[3]: *** [filterBam.o] Error 1
make[3]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs'
make: *** [all] Error 2
ADD COMMENTlink modified 4 months ago by Philipp Bayer6.5k • written 4 months ago by ashaneev0710
1

Switch to conda installations if not already

  1. First install miniconda using this link

    https://docs.conda.io/en/latest/miniconda.html

  2. Install augustus

   conda install -c bioconda augustus 
ADD REPLYlink modified 4 months ago • written 4 months ago by lakhujanivijay4.5k

Seconding conda, if you don't want conda it's a common error message for which are numerous workarounds on the internet, see for example https://iamphioxus.org/2017/05/08/installing-augustus-with-manual-bamtools-installation/

(I also edited the code in the OP post)

ADD REPLYlink written 4 months ago by Philipp Bayer6.5k

Thanks for your reply.. I've edited the makefile (filterbam/src), but again it shows the same error.

make[3]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam/src'
g++     -std=c++0x  -c filterBam.cc -o filterBam.o -I/home/dcb/Documents/EV/Maker/bamtools/include/bamtools -Iheaders -I./bamtools
filterBam.cc:14:31: fatal error: api/BamReader.h: No such file or directory
 #include <api/BamReader.h>    
                               ^
compilation terminated.
make[3]: *** [filterBam.o] Error 1
ADD REPLYlink written 4 months ago by ashaneev0710

Thanks for your reply. I also tried with conda install.But while checking with augustus it shows that

 augustus: error while loading shared libraries: libboost_iostreams.so.1.60.0: cannot open shared object file: No such file or directory
ADD REPLYlink modified 4 months ago • written 4 months ago by ashaneev0710

conda install boost could solve this (perhaps then reinstalling augustus)

ADD REPLYlink written 4 months ago by Philipp Bayer6.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1296 users visited in the last hour