errors running Trinity

[bioBob]

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

[arvid]

Does almost all the Butterfly jobs fail or only a few? If only a few, try to restart them with larger heap space - since you are only running four parallel jobs on a 1TB machine you can allow a lot more than 10 GB/job...

BTW the switch "--run_butterfly" indicates that you are running an old release of Trinity - since the Oct 29 release that switch is obsolete. You might want to try the latest and greatest release...

[bioBob]

Most of the Butterfly jobs fail. I think my sysadmin took the download that sourceforge had as the latest release. Are the newer ones there full releases or ??

I will try both the above, thanks.

For the butterfly jobs that fail, when I look in the fasta file in the job directory, there are not many sequences, less than 10 in several of them.

[jsimba]

java error running trinity

Hi every one,

Im running this line:

r2013-02-25$ Trinity.pl --seqType fq --JM 10G --single ../libraries/noninoculated/M6_N_GCCAAT_L002_R1_001.fastq M8_N_ACTTGA_L002_R1_001.fastq M8_N_ACTTGA_L002_R1_002.fastq --CPU 6

and appears:

Running Java Tests
CMD: java -Xmx64m -jar /usr/local/bin/util/ExitTester.jar 0
Error: Unable to access jarfile /usr/local/bin/util/ExitTester.jar
Error, cmd: java -Xmx64m -jar /usr/local/bin/util/ExitTester.jar 0 died with ret 256 at /usr/local/bin/Trinity.pl line 1476

Error encountered in testing for running of a simple java application. Please check your java configuration.


I read before that this error could be due to to the directory of trinity but I ran again from that directory and the error persists so I dont know if there is someting wrong with the java configuration or not

thanks