Hi,
I am having some difficulty running trinity.
Here is my command:
Trinity.pl --seqType fq --single $liver_FILE --CPU 4 --run_butterfly --bflyHeapSpace 10G
I am running this on a 1TB RAM machine with openSUSE.
There are a lot of the following errors, I included one line that appears to have worked followed by one of the errors:
RUNNING: java -Xmx10G -jar /apps/packages/bio/trinity/2011-08-20/Butterfly/Butterfly.jar -N 50933983 -L 200 -F 300 -C chrysalis/RawComps.22/comp45253
RUNNING: java -Xmx10G -jar /apps/packages/bio/trinity/2011-08-20/Butterfly/Butterfly.jar -N 50933983 -L 200 -F 300 -C chrysalis/RawComps.15/comp30303
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:60)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
at java.lang.reflect.Method.invoke(Method.java:611)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 1
at TransAssembly_allProbPaths.readAndMapSingleRead(TransAssembly_allProbPaths.java:2911)
at TransAssembly_allProbPaths.getReadStarts(TransAssembly_allProbPaths.java:2842)
at TransAssembly_allProbPaths.main(TransAssembly_allProbPaths.java:540)
... 5 more
Error, command: java -Xmx10G -jar /apps/packages/bio/trinity/2011-08-20/Butterfly/Butterfly.jar -N 50933983 -L 200 -F 300 -C chrysalis/RawComps.21/comp42886 died with ret 256FAILED[67879]: java -Xmx10G -jar /apps/packages/bio/trinity/2011-08-20/Butterfly/Butterfly.jar -N 50933983 -L 200 -F 300 -C chrysalis/RawComps.21/comp42886
NE1 have some suggestions? The data consists of 300M reads of Illumina data concatenated into a single fastq file. The read length is somewhat short at 42 bp.
Thanks.
Bob
I am having some difficulty running trinity.
Here is my command:
Trinity.pl --seqType fq --single $liver_FILE --CPU 4 --run_butterfly --bflyHeapSpace 10G
I am running this on a 1TB RAM machine with openSUSE.
There are a lot of the following errors, I included one line that appears to have worked followed by one of the errors:
RUNNING: java -Xmx10G -jar /apps/packages/bio/trinity/2011-08-20/Butterfly/Butterfly.jar -N 50933983 -L 200 -F 300 -C chrysalis/RawComps.22/comp45253
RUNNING: java -Xmx10G -jar /apps/packages/bio/trinity/2011-08-20/Butterfly/Butterfly.jar -N 50933983 -L 200 -F 300 -C chrysalis/RawComps.15/comp30303
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:60)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
at java.lang.reflect.Method.invoke(Method.java:611)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 1
at TransAssembly_allProbPaths.readAndMapSingleRead(TransAssembly_allProbPaths.java:2911)
at TransAssembly_allProbPaths.getReadStarts(TransAssembly_allProbPaths.java:2842)
at TransAssembly_allProbPaths.main(TransAssembly_allProbPaths.java:540)
... 5 more
Error, command: java -Xmx10G -jar /apps/packages/bio/trinity/2011-08-20/Butterfly/Butterfly.jar -N 50933983 -L 200 -F 300 -C chrysalis/RawComps.21/comp42886 died with ret 256FAILED[67879]: java -Xmx10G -jar /apps/packages/bio/trinity/2011-08-20/Butterfly/Butterfly.jar -N 50933983 -L 200 -F 300 -C chrysalis/RawComps.21/comp42886
NE1 have some suggestions? The data consists of 300M reads of Illumina data concatenated into a single fastq file. The read length is somewhat short at 42 bp.
Thanks.
Bob
Comment