Trinity failed
Fangqin Zeng
I ran trinity with about 70 million data from RNA-seq. I got following problems:
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.
Much appreciated for any suggestions.
Fangqin