GATK CollectReadCounts UnsatisfiedLinkError hdf5 java

Question

[chrisgr]

I'm trying to run GATK's CollectReadCounts.

It looks like running propperly but then it stop and gives the following error message:

java.lang.UnsatisfiedLinkError: /tmp/libjhdf5.2.11.06741640809408344263.so: /tmp/libjhdf5.2.11.06741640809408344263.so: failed to map segment from shared object: Operation not permitted

Can't seem to find anyone with the same problem anywhere on the internet please help Here is what the terminal looks like:

09:38:16.391 INFO  ProgressMeter -       chr11:72822055              1.8              43610000       23779058.1
09:38:26.393 INFO  ProgressMeter -       chr12:55636882              2.0              48036000       24009996.7
09:38:36.398 INFO  ProgressMeter -       chr14:57208376              2.2              52254000       24109070.8
09:38:46.398 INFO  ProgressMeter -       chr15:89326908              2.3              56200000       24077974.9
09:38:56.399 INFO  ProgressMeter -       chr16:87492006              2.5              60268000       24099809.4
09:39:06.400 INFO  ProgressMeter -       chr18:12546678              2.7              64492000       24177397.9
09:39:16.400 INFO  ProgressMeter -       chr19:44500323              2.8              68990000       24342681.7
09:39:26.400 INFO  ProgressMeter -       chr20:62308491              3.0              73309000       24429954.4
09:39:36.418 INFO  ProgressMeter -        chrX:73213111              3.2              77333000       24412595.7
09:39:41.181 INFO  CollectReadCounts - 0 read(s) filtered by: WellformedReadFilter
119131 read(s) filtered by: MappedReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
0 read(s) filtered by: NotDuplicateReadFilter
4803825 read(s) filtered by: MappingQualityReadFilter
4922956 total reads filtered
09:39:41.182 INFO  ProgressMeter -       chrX:156009831              3.2              79223571       24397878.4
09:39:41.182 INFO  ProgressMeter - Traversal complete. Processed 79223571 total reads in 3.2 minutes.
09:39:41.182 INFO  CollectReadCounts - Writing read counts to /data/Ldrive/userdirs/Christian/mapping_and_analysis_pipelinefiles/bijlsma/copynumberanalysis_bijlsma/sandbox/tumor.counts.hdf5...
log4j:WARN No appenders could be found for logger (org.broadinstitute.hdf5.HDF5Library).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
java.lang.UnsatisfiedLinkError: /tmp/libjhdf5.2.11.08777680362409959995.so: /tmp/libjhdf5.2.11.08777680362409959995.so: failed to map segment from shared object: Operation not permitted
        at java.base/jdk.internal.loader.NativeLibraries.load(Native Method)
        at java.base/jdk.internal.loader.NativeLibraries$NativeLibraryImpl.open(NativeLibraries.java:388)
        at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:232)
        at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:174)
        at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2389)
        at java.base/java.lang.Runtime.load0(Runtime.java:755)
        at java.base/java.lang.System.load(System.java:1953)
        at ncsa.hdf.hdf5lib.H5.loadH5Lib(H5.java:290)
        at ncsa.hdf.hdf5lib.H5.<clinit>(H5.java:254)
        at org.broadinstitute.hdf5.HDF5Library.loadLibrary(HDF5Library.java:87)
        at org.broadinstitute.hdf5.HDF5File.<init>(HDF5File.java:77)
        at org.broadinstitute.hellbender.tools.copynumber.formats.collections.HDF5SimpleCountCollection.write(HDF5SimpleCountCollection.java:113)
        at org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection.writeHDF5(SimpleCountCollection.java:174)
        at org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts.onTraversalSuccess(CollectReadCounts.java:206)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1099)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)