Question: Issue with bowtie2-align during installation of bowtie2
0
gravatar for seta
2.2 years ago by
seta1.1k
Sweden
seta1.1k wrote:

Hi all,

I downloaded the latest version of bowtie2 (source file) and try to install it on linux. But after typing make I got the following error:

/opt/gridengine/default/spool/gpuLD-8-3/active_jobs/17486.1/pe_hostfile
gpuLD-8-3
/opt/gridengine/default/spool/gpuLD-8-3/job_scripts/17486: line 11: /home/mmoazam/wrkdir/software/bowtie2-2.3.0: is a directory
rm: cannot remove `/tmp/17486.1.LDhosts.q/rsh': No such file or directory
/opt/gridengine/default/spool/gpuLD-8-3/active_jobs/17487.1/pe_hostfile
gpuLD-8-3
g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
        -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
         -I third_party \
        -o bowtie2-build-s bt2_build.cpp \
        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
        -lpthread -ltbb -ltbbmalloc_proxy 
/bin/sh: g++: command not found
make: *** [bowtie2-build-s] Error 127
rm: cannot remove `/tmp/17487.1.LDhosts.q/rsh': No such file or directory
/opt/gridengine/default/spool/gpuLD-8-3/active_jobs/17488.1/pe_hostfile
gpuLD-8-3
g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
        -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
         -I third_party \
        -o bowtie2-build-s bt2_build.cpp \
        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
        -lpthread -ltbb -ltbbmalloc_proxy 
/bin/sh: g++: command not found
make: *** [bowtie2-build-s] Error 127
rm: cannot remove `/tmp/17488.1.LDhosts.q/rsh': No such file or directory
/opt/gridengine/default/spool/gpuLD-8-3/active_jobs/17489.1/pe_hostfile
gpuLD-8-3
g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
        -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
         -I third_party \
        -o bowtie2-build-s bt2_build.cpp \
        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
        -lpthread -ltbb -ltbbmalloc_proxy 
/bin/sh: g++: command not found
make: *** [bowtie2-build-s] Error 127
rm: cannot remove `/tmp/17489.1.LDhosts.q/rsh': No such file or directory

and when I tried to call bowtie2, it says:

(ERR): Expected bowtie2 to be in same directory with bowtie2-align:
/gfs-dist/mmoazam/software/bowtie2-2.3.0/
Exiting now ...

and when I type "which bowtie2", it says:

/usr/bin/which: no bowtie2 in (/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bin:/opt/bio/hmmer/bin:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glimmer/bin:/opt/bio/glimmer/scripts:/opt/bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodocksuite/bin:/opt/bio/wgs/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java/latest/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin/linux-x64:/home/mmoazam/bin)

Could you please help me what happen and how to solve it?

Thanks in advance

ADD COMMENTlink modified 18 months ago by Karma200 • written 2.2 years ago by seta1.1k

One reason to download the pre-compiled binary and not have to worry about some of this stuff. You will have to install libtbb2 library though.

Edit: My suggestion has already been discussed in a different thread by seta : Issue with installing bowtie2

You may have to talk with your sys admins for g++ (if it is missing). In that case you may as well have them install bowtie2.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by genomax65k

Actually, the pre-complied bowtie didn't work on our cluster. Our admin advised me the program must be compiled on the same system to work well. I thought that the current problem is related to bowtie-align not tbb library, so I created the new post.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by seta1.1k

But if you need to get a compiler installed then admins could help you with compilation of bowtie2 as well.

Using a privately compiled program may or may not work well, if your personal space is not accessible on all of cluster nodes.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by genomax65k

If g++ isn't installed then you're going to have a tough time compiling much of anything...

ADD REPLYlink written 2.2 years ago by Devon Ryan89k

It sounds that g++ is installed. the output of "which g++" is /usr/bin/g++. So, could you please let me know what's wrong with installation of bowtie2?

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by seta1.1k

Looks like you had submitted the compile job to the job scheduler? You should compile directly on the command line! Actual bowtie2 jobs would go through the scheduler.

What's wrong is that you have not managed to get bowtie2 compiled .. likely because of above.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by genomax65k

Hi Genomax2,

Yes, that's right. I tried to compile the job via job scheduler as our admin says:"nothing will be done on the primary node and everything even compiling must be done via job scheduler", he got me crazy!. However, as you mentioned in your earlier comment, the problem was related to "tbb library" since when I compiled bowtie2 without using tbb library, it worked well. However, as this library related to parallel performance, I'm not sure about the speed of bowtie, could you please let me know if the speed of bowtie without this library is low?

Again, the admin says:"for calling the tbb library, I must be type "module load/intel" before typing "make" for compiling, is it right? however, the same error appeared when I did his advice. Since the output of "which tbb" is:

/usr/bin/which: no tbb in (/opt/openmpi/bin:/usr/lib64/qt-     3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bin:/opt/bio/hmmer/bin:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glimmer/bin:/opt/bio/glimmer/scripts:/opt/bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodocksuite/bin:/opt/bio/wgs/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java/latest/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin/linux-x64:/home/mmoazam/bin)

I guess the library isn't installed, yes? but I don't understand what admin says for calling it. Please kindly advise me on this issue.

Thanks

ADD REPLYlink written 2.2 years ago by seta1.1k

If loading the TBB module doesn't solve the problem then just compile without it. I wouldn't expect this to be a 5x difference in speed or anything.

ADD REPLYlink written 2.2 years ago by Devon Ryan89k
0
gravatar for Pierre Lindenbaum
2.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

g++: command not found

ADD COMMENTlink written 2.2 years ago by Pierre Lindenbaum118k
0
gravatar for Karma
18 months ago by
Karma200
India
Karma200 wrote:

Try following commands

​sudo apt-get install g++
​sudo apt-get install libtbb-dev
make
ADD COMMENTlink modified 18 months ago • written 18 months ago by Karma200
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