Question: errors in trinity installation
0
gravatar for citronxu
5 months ago by
citronxu10
citronxu10 wrote:

Hi there,

I tried to install trinity in my lap, which is in Ubuntu 18.04 version. I followed instructions, However, following error bumping up when I run the 'sudo make' command inside the folder where I got by unzipping the .gz file from trinityrnaseq.


Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && make
make[1]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm'
mkdir -p build
cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
-- No build type specified so building in RELEASE mode.
-- system: Linux
-- Configuring done
-- Generating done
-- Build files have been written to: /home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build
make[2]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build'
make[3]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build'
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build'
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build'
[ 32%] Built target FastaToDeBruijn
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build'
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build'
[ 67%] Built target inchworm
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build'
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build'
[100%] Built target fastaToKmerCoverageStats
make[3]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build'
Install the project...
-- Install configuration: "Release"
-- Up-to-date: ../bin/inchworm
-- Up-to-date: ../bin/FastaToDeBruijn
-- Up-to-date: ../bin/fastaToKmerCoverageStats
make[2]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm/build'
make[1]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Inchworm'
cd Chrysalis && make
make[1]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis'
mkdir -p build
cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
-- No build type specified so building in RELEASE mode.
-- system: Linux
-- Configuring done
-- Generating done
-- Build files have been written to: /home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build
make[2]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
make[3]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
[ 21%] Built target GraphFromFasta
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
[ 33%] Built target CreateIwormFastaBundle
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
[ 48%] Built target Chrysalis
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
[ 65%] Built target QuantifyGraph
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
[ 78%] Built target ReadsToTranscripts
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
[100%] Built target BubbleUpClustering
make[3]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
Install the project...
-- Install configuration: "Release"
-- Up-to-date: ../bin/Chrysalis
-- Up-to-date: ../bin/GraphFromFasta
-- Up-to-date: ../bin/QuantifyGraph
-- Up-to-date: ../bin/ReadsToTranscripts
-- Up-to-date: ../bin/BubbleUpClustering
-- Up-to-date: ../bin/CreateIwormFastaBundle
make[2]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis/build'
make[1]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/Chrysalis'
cd trinity-plugins && make trinity_essentials
make[1]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins'
cd seqtk-trinity && make CXX=g++ CC=gcc
make[2]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/seqtk-trinity'
gcc -g -Wall -O2 -Wno-unused-function seqtk.c -o seqtk-trinity -lz -lm
make[2]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/seqtk-trinity'
mv seqtk-trinity/seqtk-trinity ./BIN/.
tar -zxvf "ParaFly-0.1.0".tar.gz && \
cd "ParaFly-0.1.0" && sh ./configure --prefix=`pwd` CXX=g++ CC=gcc CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && make install && \
cp bin/ParaFly ../BIN/
ParaFly-0.1.0/
ParaFly-0.1.0/LICENSE
ParaFly-0.1.0/Makefile
ParaFly-0.1.0/Makefile.am
ParaFly-0.1.0/Makefile.in
ParaFly-0.1.0/README.md
ParaFly-0.1.0/aclocal.m4
ParaFly-0.1.0/bin/
ParaFly-0.1.0/bin/ParaFly
ParaFly-0.1.0/config.h
ParaFly-0.1.0/config.h.in
ParaFly-0.1.0/config.log
ParaFly-0.1.0/config.status
ParaFly-0.1.0/configure
ParaFly-0.1.0/configure.ac
ParaFly-0.1.0/depcomp
ParaFly-0.1.0/install-sh
ParaFly-0.1.0/missing
ParaFly-0.1.0/src/
ParaFly-0.1.0/src/.deps/
ParaFly-0.1.0/src/.deps/ParaFly.Po
ParaFly-0.1.0/src/.deps/argProcessor.Po
ParaFly-0.1.0/src/Makefile
ParaFly-0.1.0/src/Makefile.am
ParaFly-0.1.0/src/Makefile.in
ParaFly-0.1.0/src/ParaFly.cpp
ParaFly-0.1.0/src/argProcessor.cpp
ParaFly-0.1.0/src/argProcessor.hpp
ParaFly-0.1.0/stamp-h1
ParaFly-0.1.0/test/
ParaFly-0.1.0/test/Makefile
ParaFly-0.1.0/test/cmds.txt
ParaFly-0.1.0/test/rand_exit.pl
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for library containing cos... none required
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make[2]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0'
Making install in src
make[3]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0/src'
g++ -DHAVE_CONFIG_H -I. -I..    -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -fopenmp -MT ParaFly.o -MD -MP -MF .deps/ParaFly.Tpo -c -o ParaFly.o ParaFly.cpp
mv -f .deps/ParaFly.Tpo .deps/ParaFly.Po
g++ -DHAVE_CONFIG_H -I. -I..    -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -fopenmp -MT argProcessor.o -MD -MP -MF .deps/argProcessor.Tpo -c -o argProcessor.o argProcessor.cpp
mv -f .deps/argProcessor.Tpo .deps/argProcessor.Po
g++ -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -fopenmp   -o ParaFly ParaFly.o argProcessor.o  
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0/src'
test -z "/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0/bin" || /bin/mkdir -p "/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0/bin"
  /usr/bin/install -c ParaFly '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0/bin'
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0/src'
make[3]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0/src'
make[3]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0'
make[4]: Entering directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0'
make[3]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0'
make[2]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins/ParaFly-0.1.0'
ln -sf Trimmomatic-0.36 Trimmomatic
cd htslib && autoreconf && ./configure --prefix=`pwd` && make && make install
/bin/sh: 1: autoreconf: not found
Makefile:29: recipe for target 'htslib.ok' failed
make[1]: *** [htslib.ok] Error 127
make[1]: Leaving directory '/home/citronxu/Downloads/trinityrnaseq-v2.10.0/trinity-plugins'
Makefile:36: recipe for target 'trinity_essentials' failed
make: *** [trinity_essentials] Error 2

Also after facing this error, I checked things needed and their version:
gcc is already the newest version (4:7.4.0-1ubuntu2.3).
cmake version 3.17.0
CMake suite maintained and supported by Kitware kitware.com/cmake)

appreciate any help.

software error • 372 views
ADD COMMENTlink modified 5 months ago by 18315057230 • written 5 months ago by citronxu10
1

Hi,

Where did you copy-paste this error from? This seems to be lifted of some sort of old forum post, it was surely not copy-pasted from a plain text log file/console or typed by hand.

ADD REPLYlink written 5 months ago by RamRS30k

Hello,

No, it is not from any forum lol. Since simply using copy and paste makes the whole return display in a mess way, I use copy it as HTML for better showing.

ADD REPLYlink written 5 months ago by citronxu10
1

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

ADD REPLYlink written 5 months ago by RamRS30k

Thanks! I'll definitely do it next time. A lot thanks again.

ADD REPLYlink written 5 months ago by citronxu10

Consider this hardware requirement note from Trinity developers.

A basic recommendation is to have ~1G of RAM per ~1M pairs of Illumina reads

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax89k

why donnot you use conda platform to install trinity

ADD REPLYlink written 5 months ago by 18315057230
3
gravatar for cschu181
5 months ago by
cschu1812.5k
cschu1812.5k wrote:

Try sudo apt-get install autoconf (See this post).

That said, I don't think trinity is something you can actually run properly on a laptop...

ADD COMMENTlink modified 5 months ago by RamRS30k • written 5 months ago by cschu1812.5k

problem solved, thanks!

ADD REPLYlink written 5 months ago by citronxu10

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

ADD REPLYlink written 5 months ago by genomax89k

Thank you for the guide!:)

ADD REPLYlink written 5 months ago by citronxu10
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