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mozack / abra

Assembly Based ReAligner
MIT License
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java.lang.UnsatisfiedLinkError #16

Closed preciserobot closed 9 years ago

preciserobot commented 9 years ago

Hi, I get this error on some of our computation nodes but can't figure out what is going wrong/ is different.

/share/java/jdk1.7.0/bin/java -Xmx4g -jar abra-0.92-SNAPSHOT-jar-with-dependencies.jar --in da82e52f.bam --out da82e52f.realigned.unsorted.bam --ref human_g1k_v37.fasta --bwa-ref human_g1k_v37.fasta --threads 4 --targets final_baitcapture_moderate_1_Regions.bed --working /tmp/tmp_5d98 --mad 250 --mapq 10 --mer 0.1 --mur 500000 --rcf 0.01

Exception in thread "main" java.lang.UnsatisfiedLinkError: > /tmp/tmp_5d98/libAbra.so: /tmp/tmp_5d98/libAbra.so: undefined symbol: _ZZN6google11sparsegroupIPKcLt48ENS_27libc_allocator_with_reallocIS2_EEE12bits_in_charEhE7bits_in at java.lang.ClassLoader$NativeLibrary.load(Native Method) at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1928) at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1825) at java.lang.Runtime.load0(Runtime.java:792) at java.lang.System.load(System.java:1059) at abra.NativeLibraryLoader.load(NativeLibraryLoader.java:45) at abra.ReAligner.init(ReAligner.java:1093) at abra.ReAligner.reAlign(ReAligner.java:116) at abra.ReAligner.run(ReAligner.java:1214) at abra.Abra.main(Abra.java:12)

I tried Java 1.7.0 and 1.8.0 with the same outcome.

Thanks for your help

preciserobot commented 9 years ago

This error occurred using your prebuilt jar. Building it from source solved the problem so far.

mozack commented 9 years ago

OK. Let me know if you run into any further trouble.