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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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sthlm2UUSNP NoClassDefFound #25

Closed mariogiov closed 9 years ago

mariogiov commented 9 years ago

Alright I'm trying to use sthlm2UUSNP on the flowcellrun level, e.g. the format sthlm2UUSNP -i {input_dir} -o {output_dir} -f {flowcell} and it's failing. At first I thought this was a FileAlreadyExistsException but I looked more closely and it looks like it is actually a definition missing problem. Just as background though, the actual command resembles:

sthlm2UUSNP -i /proj/a2010002/nobackup/mario/analysis_ready/DATA/G.Grigelioniene_14_01 -o /proj/a2010002/nobackup/mario/analysis_ready/DATA_UUSNP/G.Grigelioniene_14_01 -f 140528_BC423WACXX

The input directory:

/proj/a2010002/nobackup/mario/analysis_ready/DATA/G.Grigelioniene_14_01/
└── P1142_101
    └── A
        └── 140528_BC423WACXX
            ├── P1142_101_NoIndex_L001_R1_001.fastq.gz
            ├── P1142_101_NoIndex_L001_R2_001.fastq.gz
            ├── P1142_101_NoIndex_L002_R1_001.fastq.gz
            ├── P1142_101_NoIndex_L002_R2_001.fastq.gz
            ├── P1142_101_NoIndex_L003_R1_001.fastq.gz
            ├── P1142_101_NoIndex_L003_R2_001.fastq.gz
            ├── P1142_101_NoIndex_L004_R1_001.fastq.gz
            └── P1142_101_NoIndex_L004_R2_001.fastq.gz

The output directory does not exist:

(ngi)mario@nestor1$ ls /proj/a2010002/nobackup/mario/analysis_ready/DATA_UUSNP/G.Grigelioniene_14_01
ls: cannot access /proj/a2010002/nobackup/mario/analysis_ready/DATA_UUSNP/G.Grigelioniene_14_01: No such file or directory
(ngi)mario@nestor1$ ls /proj/a2010002/nobackup/mario/analysis_ready/DATA_UUSNP/
ls: cannot access /proj/a2010002/nobackup/mario/analysis_ready/DATA_UUSNP/: No such file or directory

The traceback:

Exception in thread "main" java.lang.NoClassDefFoundError: java/nio/file/FileAlreadyExistsException
        at molmed.apps.Sthlm2UUSNP.main(Sthlm2UUSNP.scala)
Caused by: java.lang.ClassNotFoundException: java.nio.file.FileAlreadyExistsException
        at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
        ... 1 more
mariogiov commented 9 years ago

Yeah it does this with everything

(ngi)mario@nestor1$ sthlm2UUSNP your mom goes to college
Exception in thread "main" java.lang.NoClassDefFoundError: java/nio/file/FileAlreadyExistsException
        at molmed.apps.Sthlm2UUSNP.main(Sthlm2UUSNP.scala)
Caused by: java.lang.ClassNotFoundException: java.nio.file.FileAlreadyExistsException
        at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
        ... 1 more
mariogiov commented 9 years ago

Oh it's a Java problem. nm. JAVA! which is to say I was using the wrong version again

johandahlberg commented 9 years ago

A little suggestion is adding: module load java/sun_jdk1.7.0_25 to your .bashrc, then this shouldn't bother you anymore (on Uppmax at least). +1 for funny input arguments! :smile: