install problems with trinity v2.2.0
Fangqin Zeng
Performing Unit Tests of Build
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JellyFish: has been Installed Properly
Inchworm: has been Installed Properly
Chrysalis Installation appears to have FAILED
QuantifyGraph Installation appears to have FAILED
GraphFromFasta Installation appears to have FAILED
ReadsToTranscripts Installation appears to have FAILED
fastool: has been Installed Properly
parafly: has been Installed Properly
samtools-0.1.19 has been Installed Properly
I try:
cd Chrysalis
make clean
make
When type make clean, the outputs are:
Makefile:81: using g++ version 4.4.7
Makefile:82: --------------------------------------------------------
./MakeDepend: /opt/hds/Base/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by ./MakeDepend)
make: *** [depend] Error 1
for file in ; do rm -f ./$file; done
rm -f MakeDepend ./MakeDepend contigs.out my.permanent.log.file \
core a.out Makefile.bak bsubin BasevectorTables.h ./checkLock
find obj -name '*.o' -exec rm {} \; || /bin/true
When type make, the outputs are:
Makefile:81: using g++ version 4.4.7
Makefile:82: --------------------------------------------------------
./MakeDepend.cc: In member function ‘bool makefile_builder::dependency::operator<(const makefile_builder::dependency&) const’:
./MakeDepend.cc:94: warning: suggest parentheses around ‘&&’ within ‘||’
./MakeDepend.cc: In member function ‘bool makefile_builder::subdir_and_target::operator<(const makefile_builder::subdir_and_target&) const’:
./MakeDepend.cc:131: warning: suggest parentheses around ‘&&’ within ‘||’
./MakeDepend.cc: In function ‘int main(int, char**)’:
./MakeDepend.cc:223: warning: deprecated conversion from string constant to ‘char*’
./MakeDepend.cc: In member function ‘void makefile_builder::DumpDependencies(const std::string&)’:
./MakeDepend.cc:492: warning: suggest parentheses around ‘&&’ within ‘||’
./MakeDepend.cc:493: warning: suggest parentheses around ‘&&’ within ‘||’
./MakeDepend.cc: In member function ‘bool makefile_builder::FileIsHeader(const std::string&) const’:
./MakeDepend.cc:1342: warning: suggest parentheses around ‘&&’ within ‘||’
./MakeDepend: /opt/hds/Base/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by ./MakeDepend)
make: *** [depend] Error 1
make: Nothing to be done for `all'.
Can anybody give me some suggestions?
Thanks,
Fang
Fulton, Ben
What flavor of Linux are you trying to compile on?
--
Ben Fulton
Research Technologies
Scientific Applications and Performance Tuning
Indiana University
E-Mail: befu...@iu.edu
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Fangqin Zeng
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Fangqin Zeng
Wednesday, May 4, 2016: 20:18:47 CMD: /aafc-aac/home/users-data/mpp/trinityrnaseq-2.2.0/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 6 -v
Number of Commands: 134043
succeeded(44543) 33.2304% completed.
We are sorry, commands in file: [failed_butterfly_commands.81344.txt] failed. :-(
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.HashMap.createEntry(HashMap.java:897)
at java.util.HashMap.addEntry(HashMap.java:884)
at java.util.HashMap.put(HashMap.java:505)
at java.util.HashSet.add(HashSet.java:217)
at PairPath._cache_path_nodes(PairPath.java:70)
at PairPath.<init>(PairPath.java:30)
at TransAssembly_allProbPaths.update_PairPaths_using_overlapDAG_refined_paths(TransAssembly_allProbPaths.java:1837)
at TransAssembly_allProbPaths.create_DAG_from_OverlapLayout(TransAssembly_allProbPaths.java:1590)
at TransAssembly_allProbPaths.main(TransAssembly_allProbPaths.java:918)
Trinity run failed. Must investigate error above.
succeeded(55018), failed(1) 41.0458% completed.
We are sorry, commands in file: [failed_butterfly_commands.79373.txt] failed. :-(
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.ArrayList.iterator(ArrayList.java:814)
at java.util.AbstractList.hashCode(AbstractList.java:540)
at PairPath.hashCode(PairPath.java:95)
at java.util.HashMap.hash(HashMap.java:362)
at java.util.HashMap.put(HashMap.java:492)
at TransAssembly_allProbPaths.update_PairPaths_using_overlapDAG_refined_paths(TransAssembly_allProbPaths.java:1838)
at TransAssembly_allProbPaths.create_DAG_from_OverlapLayout(TransAssembly_allProbPaths.java:1590)
at TransAssembly_allProbPaths.main(TransAssembly_
allProbPaths.java:918)
Trinity run failed. Must investigate error above.
/aafc-aac/home/users-data/mpp/trinityrnaseq-2.2.0/util/support_scripts/../../Trinity --single "/aafc-aac/home/users-data/zengf/RNAseqlate/trinity_out_dir/read_partitions/Fb_0/CBin_604/c60456.trinity.reads.fa" --output "/aafc-aac/home/users-data/zengf/RNAseqlate/trinity_out_dir/read_partitions/Fb_0/CBin_604/c60456.trinity.reads.fa.out" --CPU 1 --max_memory 1G --seqType fa --trinity_complete --normalize_reads
The outputs :
We are sorry, commands in file: [failed_butterfly_commands.7542.txt] failed. :-(
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.Arrays.copyOf(Arrays.java:2367)
at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:415)
at java.lang.StringBuilder.append(StringBuilder.java:132)
at java.lang.StringBuilder.append(StringBuilder.java:128)
at java.util.AbstractCollection.toString(AbstractCollection.java:458)
at java.lang.String.valueOf(String.java:2847)
at java.lang.StringBuilder.append(StringBuilder.java:128)
at java.util.AbstractCollection.toString(AbstractCollection.java:458)
at java.lang.String.valueOf(String.java:2847)
at java.lang.StringBuilder.append(StringBuilder.java:128)
at PairPath.toString(PairPath.java:84)
at java.lang.String.valueOf(String.java:2847)
at java.lang.StringBuilder.append(StringBuilder.java:128)
at TransAssembly_allProbPaths.update_PairPaths_using_overlapDAG_refined_paths(TransAssembly_allProbPaths.java:1803)
at TransAssembly_allProbPaths.create_DAG_from_OverlapLayout(TransAssembly_allProbPaths.java:1590)
at TransAssembly_allProbPaths.main(TransAssembly_allProbPaths.java:918)
Trinity run failed. Must investigate error above.
Then I run the Trinity commnads which showed error as following:
We are sorry, commands in file: [failed_butterfly_commands.8378.txt] failed. :-(
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.Arrays.copyOf(Arrays.java:2219)
at java.util.ArrayList.grow(ArrayList.java:242)
at java.util.ArrayList.ensureExplicitCapacity(ArrayList.java:216)
at java.util.ArrayList.ensureCapacityInternal(ArrayList.java:208)
at java.util.ArrayList.add(ArrayList.java:440)
at PathWithOrig.align_path_by_orig_id(PathWithOrig.java:76)
at TransAssembly_allProbPaths.get_all_possible_updated_path_mappings(TransAssembly_allProbPaths.java:1931)
at TransAssembly_allProbPaths.update_PairPaths_using_overlapDAG_refined_paths(TransAssembly_allProbPaths.java:1816)
at TransAssembly_allProbPaths.create_DAG_from_OverlapLayout(TransAssembly_allProbPaths.java:1590)
at TransAssembly_allProbPaths.main(TransAssembly_allProbPaths.java:918)
Trinity run failed. Must investigate error above.
succeeded(0), failed(1) 100% completed.
We are sorry, commands in file: [FailedCommands] failed. :-(
Trinity run failed. Must investigate error above.
Can you give me some suggestions?
Much appreciated.
Fangqin
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