miraligner/Main : Unsupported major.minor version 52.0

[keenhl]

Hi, I am trying to run the srnaseq pipeline and I get the following JAVA error.

Do miRNA annotation for /keenhl/project3/project3/work/trimmed/10_18-063_100_20190114000_S10_L003/10_18-063_100_20190114000_S10_L003_R1_001.clean_trimmed.fastq
[2019-01-24T17:37Z] Exception in thread "main" java.lang.UnsupportedClassVersionError: miraligner/Main : Unsupported major.minor version 52.0
[2019-01-24T17:37Z] at java.lang.ClassLoader.defineClass1(Native Method)
[2019-01-24T17:37Z] at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
[2019-01-24T17:37Z] at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
[2019-01-24T17:37Z] at java.net.URLClassLoader.defineClass(URLClassLoader.java:442)
[2019-01-24T17:37Z] at java.net.URLClassLoader.access$100(URLClassLoader.java:64)
[2019-01-24T17:37Z] Uncaught exception occurred

here are the installed versions of JAVA

java -version

openjdk version "1.8.0_161"
OpenJDK Runtime Environment (build 1.8.0_161-b14)
OpenJDK 64-Bit Server VM (build 25.161-b14, mixed mode)

./bcbio/stable/anaconda/bin/java -version

openjdk version "1.8.0_192"
OpenJDK Runtime Environment (Zulu 8.33.0.1-linux64) (build 1.8.0_192-b01)
OpenJDK 64-Bit Server VM (Zulu 8.33.0.1-linux64) (build 25.192-b01, mixed mode)

if I echo $JAVA_HOME, the result is blank

bcbio version

I am running the latest development version of bcbio (upgraded earlier today)

[lpantano]

Hi, sorry about this issue. Can you get the command line from the log/bcbio-nextgen-command.log file. Any of the one calling miraligner will be enough. Thanks! Lorena Pantano, P.h.D Research Scientist Biostatistics Department Harvard T.H. Chan School of Public Health https://mirtop.github.io https://lpantano.github.io I'll be out of office from Dec-17th to Jan9th

…

On Thu, Jan 24, 2019 at 3:02 PM keenhl ***@***.***> wrote: Hi, I am trying to run the srnaseq pipeline and I get the following JAVA error. Do miRNA annotation for /keenhl/project3/project3/work/trimmed/10_18-063_100_20190114000_S10_L003/10_18-063_100_20190114000_S10_L003_R1_001.clean_trimmed.fastq [2019-01-24T17:37Z] Exception in thread "main" java.lang.UnsupportedClassVersionError: miraligner/Main : Unsupported major.minor version 52.0 [2019-01-24T17:37Z] at java.lang.ClassLoader.defineClass1(Native Method) [2019-01-24T17:37Z] at java.lang.ClassLoader.defineClass(ClassLoader.java:803) [2019-01-24T17:37Z] at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) [2019-01-24T17:37Z] at java.net.URLClassLoader.defineClass(URLClassLoader.java:442) [2019-01-24T17:37Z] at java.net.URLClassLoader.access$100(URLClassLoader.java:64) [2019-01-24T17:37Z] Uncaught exception occurred here are the installed versions of JAVA java -version openjdk version "1.8.0_161" OpenJDK Runtime Environment (build 1.8.0_161-b14) OpenJDK 64-Bit Server VM (build 25.161-b14, mixed mode) ./bcbio/stable/anaconda/bin/java -version openjdk version "1.8.0_192" OpenJDK Runtime Environment (Zulu 8.33.0.1-linux64) (build 1.8.0_192-b01) OpenJDK 64-Bit Server VM (Zulu 8.33.0.1-linux64) (build 25.192-b01, mixed mode) if I echo $JAVA_HOME, the result is blank bcbio version I am running the latest development version of bcbio (upgraded earlier today) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2646>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HNTEKrUzRONgA_pce2hqqLAtGVRHks5vGhFSgaJpZM4aRnJf> .

[keenhl]

Thanks.

[2019-01-24T01:35Z] unset JAVA_HOME && export PATH=/Shared/Bioinformatics/data/keenhl/bcbio/stable/anaconda/bin:$PATH && /Shared/Bioinformatics/data/keenhl/bcbio/stable/galaxy/../anaconda/bin/miraligner -Xms750m -Xmx3500m -freq -sub 1 -trim 3 -add 3 -minl 16 -s hsa -i /Shared/Bioinformatics/data/keenhl/project3/project3/work/trimmed/10_18-063_100_20190114000_S10_L003/10_18-063_100_20190114000_S10_L003_R1_001.clean_trimmed.fastq -db /Shared/Bioinformatics/data/keenhl/bcbio/stable/genomes/Hsapiens/hg19/srnaseq -o /Shared/Bioinformatics/data/keenhl/project3/project3/work/bcbiotx/tmp2Re4JC/10_18-063_100_20190114000_S10_L003

[lpantano]

Hi,

I would try these different strategies:

1-make sure the last version of miraligner is installed:

bcbio_conda update -c conda-forge -c biodonca seqbuster

2- run the command locally to reproduce the error

I got the same version than you show and seqbuster 3.1-2 and all seems to work.

Let me know if the update doesn't fix the error.

[keenhl]

1. Updated miraligner. Same error.

2. Run the command locally

I ran the following commands from the terminal. They ran correctly. When I submit the same commands as a job to the compute cluster, I get the above error. As far as I can tell, the version of Java on the compute nodes is 1.7, while on the login nodes it is 1.8.

unset JAVA_HOME && export PATH=/Shared/Bioinformatics/data/keenhl/bcbio/stable/anaconda/bin:$PATH

/Shared/Bioinformatics/data/keenhl/bcbio/stable/anaconda/bin/miraligner -Xms750m -Xmx3500m -freq -sub 1 -trim 3 -add 3 -minl 16 -s hsa -i /Shared/Bioinformatics/data/keenhl/project3/project3/work/trimmed/10_18-063_100_20190114000_S10_L003/10_18-063_100_20190114000_S10_L003_R1_001.clean_trimmed.fastq -db /Shared/Bioinformatics/data/keenhl/bcbio/stable/genomes/Hsapiens/hg19/srnaseq -o output

[lpantano]

Hi, it seems somehow it got the other java version even if we are forcing the java installed with bcbio. I will try to get help on this.

[lpantano]

Hi,

As a wild test, can you modify the file:

and comment these lines:

/Shared/Bioinformatics/data/keenhl/bcbio/stable/anaconda/bin/miraligner

if [ -z "${JAVA_HOME:=}" ]; then
  if [ -e "$JAVA_HOME/bin/java" ]; then
      java="$JAVA_HOME/bin/java"
  fi
fi

[keenhl]

Thanks. Yes, I will give it a try and let you know how it goes.

[keenhl]

I commented out the lines mentioned above, and ran the above commands. It worked without error. I will try re-running the entire pipeline.

[lpantano]

ok, let me know. That is weird because we specifically unset java_home before running.

[chapmanb]

Thanks for this help debugging. This triggered my memory that we had swapped the bash check a while back to avoid accidentally picking up java in /bin/java:

bioconda/bioconda-recipes@b726965

In the wrapper script if you swap -z for -n that should avoid the problem:

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/seqbuster/miraligner.sh#L21

Thanks for all the work debugging this.

[lpantano]

awesome! I'll do that! updating: bioconda/bioconda-recipes#13387

[keenhl]

Thanks @lpantano , @chapmanb . The entire pipeline finished successfully after making the changes referenced above.

[lpantano]

Thanks!