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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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running with java 8 dies when trying to do an exon projection in dev-mode #716

Closed nathandunn closed 8 years ago

nathandunn commented 8 years ago

Found by @deepakunni3

Steps:

Exon","sequenceList":[{"name":"Group1.1"}]}
gettting projeciton [padding:0, referenceTrack:Official Gene Set v3.2, organism:Honeybee, payload:{}, start:0, end:1382403, id:5662, projection:Exon, sequenceList:[[name:Group1.1]]]
contains the key! org.bbop.apollo.projection.ProjectionDescription@332f25d9
trying to convert []
converted []
putative sequence path name /opt/apollo/honeybee/data/tracks/Official Gene Set v3.2/{"padding":0, "projection":"Exon", "referenceTrack":"Official Gene Set v3.2", "sequenceList":[{"name":"Group1.1"}], "label":"Group1.1"}:-1..-1/trackData.json -> {"padding":0, "projection":"Exon", "referenceTrack":"Official Gene Set v3.2", "sequenceList":[{"name":"Group1.1"}], "label":"Group1.1"}:-1..-1 
JSON PROJECTION OBJECT: {"padding":0,"referenceTrack":"Official Gene Set v3.2","organism":"Honeybee","projection":"Exon","label":"Group1.1","sequenceList":[{"name":"Group1.1"}]}
gettting projeciton [padding:0, referenceTrack:Official Gene Set v3.2, organism:Honeybee, projection:Exon, label:Group1.1, sequenceList:[[name:Group1.1]]]
contains the key! org.bbop.apollo.projection.ProjectionDescription@332f25d9
found a projection 312
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x000000010e4eee40, pid=95784, tid=20739
#
# JRE version: Java(TM) SE Runtime Environment (8.0_45-b14) (build 1.8.0_45-b14)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.45-b02 mixed mode bsd-amd64 compressed oops)
# Problematic frame:
# V  [libjvm.dylib+0xeee40]
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /Users/nathandunn/repositories/Apollo/hs_err_pid95784.log
[thread 36867 also had an error]
nathandunn commented 8 years ago

It looks like this piece of code is failing when looking at the logging code:

C1: 40633 15784 3 org.bbop.apollo.projection.AbstractProjection::projectCoordinate (261 bytes)

Internal exceptions (10 events):
Event: 40.212 Thread 0x00007f8690d2b800 Exception <a 'java/lang/ClassNotFoundException': org/bbop/apollo/ProjectionService$_$tt__loadTrackJson_closure25BeanInfo> (0
x00000007a09ab690) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u45/3457/hotspot/src/share/vm/classfile/systemDi
Event: 40.212 Thread 0x00007f8690d2b800 Exception <a 'java/lang/ClassNotFoundException': org/bbop/apollo/ProjectionService$_$tt__loadTrackJson_closure25Customizer> 
(0x00000007a0a3a9b0) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u45/3457/hotspot/src/share/vm/classfile/system
Event: 40.227 Thread 0x00007f8690d2b800 Exception <a 'java/lang/ClassNotFoundException': org/bbop/apollo/projection/ProjectionSequence$_toJSONObject_closure1BeanInf
o> (0x00000007a0e2e020) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u45/3457/hotspot/src/share/vm/classfile/sys
Event: 40.228 Thread 0x00007f8690d2b800 Exception <a 'java/lang/ClassNotFoundException': org/bbop/apollo/projection/ProjectionSequence$_toJSONObject_closure1Customi
zer> (0x00000007a0ec5290) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u45/3457/hotspot/src/share/vm/classfile/s
Event: 40.232 Thread 0x00007f8690d2b800 Exception <a 'java/lang/ClassNotFoundException': org/bbop/apollo/ProjectionService$_createExonLocations_closure9BeanInfo> (0
x00000007a1048ae0) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u45/3457/hotspot/src/share/vm/classfile/systemDi
Event: 40.233 Thread 0x00007f8690d2b800 Exception <a 'java/lang/ClassNotFoundException': org/bbop/apollo/ProjectionService$_createExonLocations_closure9Customizer> 
(0x00000007a10d7a40) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u45/3457/hotspot/src/share/vm/classfile/system
Event: 40.237 Thread 0x00007f8690d2b800 Exception <a 'java/lang/ClassNotFoundException': org/bbop/apollo/ProjectionService$_extractHighLevelLocations_closure12BeanI
nfo> (0x00000007a1253d28) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u45/3457/hotspot/src/share/vm/classfile/s
Event: 40.238 Thread 0x00007f8690d2b800 Exception <a 'java/lang/ClassNotFoundException': org/bbop/apollo/ProjectionService$_extractHighLevelLocations_closure12Custo
mizer> (0x00000007a12edd70) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u45/3457/hotspot/src/share/vm/classfile
Event: 40.243 Thread 0x00007f8690d2b800 Exception <a 'java/lang/ClassNotFoundException': org/bbop/apollo/ProjectionService$_extractExonArrayLocations_closure13BeanI
nfo> (0x00000007a148f458) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u45/3457/hotspot/src/share/vm/classfile/s
Event: 40.244 Thread 0x00007f8690d2b800 Exception <a 'java/lang/ClassNotFoundException': org/bbop/apollo/ProjectionService$_extractExonArrayLocations_closure13Custo
mizer> (0x00000007a152a408) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u45/3457/hotspot/src/share/vm/classfile
nathandunn commented 8 years ago

it actually works fine when compiled / running with java 8 as a war . . . just not when using grails run-app . . . this is a known issue but really only effects development . . .

nathandunn commented 8 years ago

I think that this is related to #444

nathandunn commented 8 years ago

Closing for now. Can re-open later. I think it is fixed as part of #444.