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dieterich-lab / JACUSA2

New version of JACUSA -> 2.0
GNU General Public License v3.0
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Error with bed file and rt-arrest mode #42

Closed CDieterich closed 2 years ago

CDieterich commented 3 years ago

Dear @piechottam ,

Call: JACUSA2 Version: 2.0.0-RC22 call-2 -m 1 -A -b /prj/JACUSA2_TestField/Nanopore_HEK293/miCLIP2/union_flat.bed -q 1 -c 4 -p 10 -D -I -a D,Y -P1 FR-SECONDSTRAND -P2 FR-SECONDSTRAND -r MazF_vs_cond2_FTO_miCLIPsites_RC22_call2_result.out SRR8450805_STARmapping_uniq_rmdup.bam,SRR8450807_STARmapping_uniq_rmdup.bam,SRR8450809_STARmapping_uniq_rmdup.bam SRR8450806_STARmapping_uniq_rmdup.bam,SRR8450808_STARmapping_uniq_rmdup.bam,SRR8450810_STARmapping_uniq_rmdup.bam

java.lang.NullPointerException at lib.worker.WorkerDispatcher.hasNext(WorkerDispatcher.java:60) at lib.worker.WorkerDispatcher.run(WorkerDispatcher.java:64) at lib.util.AbstractTool.run(AbstractTool.java:60) at jacusa.JACUSA.main(JACUSA.java:96) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:61)

CDieterich commented 3 years ago

Forgot this one here..

INFO 00:00:00 Computing overlap between sequence records. java.lang.ArrayIndexOutOfBoundsException: Index 6 out of bounds for length 6 at lib.util.coordinate.provider.BedCoordinateProvider.read(BedCoordinateProvider.java:59) at lib.util.coordinate.provider.BedCoordinateProvider.(BedCoordinateProvider.java:32) at lib.util.AbstractMethod.initCoordinateProvider(AbstractMethod.java:193) at lib.cli.CLI.processArgs(CLI.java:310) at lib.util.AbstractTool.run(AbstractTool.java:48) at jacusa.JACUSA.main(JACUSA.java:96) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:61)

CDieterich commented 3 years ago

a cut -f1-3 seems to solve the issue.. but this is not nice at all.

piechottam commented 3 years ago

This has been fixed and will be available in the next release of JACUSA2.

As a temporary fix, please manually remove other columns inn BED file:

cut -f1-3 <BED> > <MODIFIED-BED>