khmer-protocols/mrnaseq/3-big-assembly.txt trinity installation

[taylorreiter]

at
khmer-protocols/mrnaseq/3-big-assembly.txt

mkdir -p ${HOME}/src cd ${HOME}/src

wget https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.4.tar.gz \ -O trinity.tar.gz tar xzf trinity.tar.gz cd trinityrnaseq*/ make |& tee trinity-build.log

Trinity subsequently fails. There seems to be a problem with Chrysalis installation. Trinity will start, and fail during read counting.

I used:
wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.tar.gz tar xzf Trinity-v2.4.0.tar.gz cd trinityrnaseq*/ make make plugins

Install java 1.8
sudo add-apt-repository ppa:webupd8team/java sudo apt-get update sudo apt-get install oracle-java8-installer

Install bowtie2
sudo apt-get install bowtie2

Test trinity
cd sample_data/test_Trinity_Assembly/ ./runMe.sh

and was successful.

[standage]

Can you post the error that was printed to the terminal when read counting failed?

[taylorreiter]

ubuntu@ip-172-31-31-125:~/projects/eelpond$ ${HOME}/src/trinityrna*/Trinity --seqType fq --max_memory 10G --CPU ${THREADS:-2} --single ~/projects/eelpond/abundfilt/*abundfilt
Trinity version: v2.0.4 ** NOTE: Latest version of Trinity is Trinity-v2.4.0, and can be obtained at: https://github.com/trinityrnaseq/trinityrnaseq/releases

Friday, March 3, 2017: 14:10:42 CMD: java -Xmx64m -jar /home/ubuntu/src/trinityrnaseq-2.0.4/util/support_scripts/ExitTester.jar 0
Friday, March 3, 2017: 14:10:42 CMD: java -Xmx64m -jar /home/ubuntu/src/trinityrnaseq-2.0.4/util/support_scripts/ExitTester.jar 1

----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------

Use of uninitialized value in array dereference at /home/ubuntu/src/trinityrnaseq-2.0.4/Trinity line 1251.
-------------------------------------------
----------- Jellyfish --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

Friday, March 3, 2017: 14:10:42 CMD: /home/ubuntu/src/trinityrnaseq-2.0.4/trinity-plugins/jellyfish/bin/jellyfish count -t 2 -m 25 -s 1533916891 --canonical single.fa 2> /dev/null Trinity run failed. Must investigate error above.

Then ran make in /my/path/to/trinity:

Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf)
&& sh ./configure --prefix=pwd && make install
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... gawk
checking whether make sets $(MAKE)... yes
checking for g++... g++
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[1]: Entering directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm'
Making install in src
make[2]: Entering directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm/src'
make[3]: Entering directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm/src'
test -z "/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm/bin" || /bin/mkdir -p "/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm/bin"
/usr/bin/install -c inchworm cigar_tweaker pull_reads_with_kmers FastaToDeBruijn fastaToKmerCoverageStats '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm/bin'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm/src'
make[2]: Leaving directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm/src'
make[2]: Entering directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm'
make[3]: Entering directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm'
make[2]: Leaving directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm'
make[1]: Leaving directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Inchworm'
cd Chrysalis && make UNSUPPORTED=yes
make[1]: Entering directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Chrysalis'
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Fri Mar 3 14:12:07 UTC 2017"' -DMAKE_OS_RELEASE='"4.2.0-30-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -fopenmp -c ./aligns/KmerAlignCore.cc -o obj/aligns/KmerAlignCore.o
./aligns/KmerAlignCore.cc:6:34: fatal error: aligns/KmerAlignCore.h: No such file or directory
compilation terminated.
Makefile:465: recipe for target 'aligns/KmerAlignCore.o' failed
make[1]: *** [aligns/KmerAlignCore.o] Error 1
make[1]: Leaving directory '/home/ubuntu/src/trinityrnaseq-2.0.4/Chrysalis'
Makefile:26: recipe for target 'chrysalis_target' failed
make: *** [chrysalis_target] Error 2'