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dieterich-lab / JACUSA2

New version of JACUSA -> 2.0
GNU General Public License v3.0
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early termination of lower-case reference file #23

Closed qwang-big closed 5 years ago

qwang-big commented 5 years ago

Hi Michael, here is what I got when providing a lower-case reference fasta

java.lang.IllegalArgumentException: Byte 99 unknown
    at lib.util.Base.valueOf(Base.java:71)
    at lib.data.storage.container.FileReferenceProvider.getReferenceBase(FileReferenceProvider.java:90)
    at lib.data.storage.container.FileReferenceProvider.getReferenceBase(FileReferenceProvider.java:68)
    at lib.data.assembler.DataAssembler.createDefaultDataContainer(DataAssembler.java:50)
    at lib.data.assembler.DataAssembler.assembleData(DataAssembler.java:39)
    at lib.util.ReplicateContainer.getNullDataContainer(ReplicateContainer.java:61)
    at lib.util.ConditionContainer.getNullDataContainer(ConditionContainer.java:42)
    at jacusa.worker.CallWorker.createParallelData(CallWorker.java:41)
...
piechottam commented 5 years ago

You probably used JACUSA2 with -R some.fasta? There is a lower case c in your FASTA(byte 99 -> c) For the time being, continue with your analysis by changing all lower case bases in FASTA to upper case. Easy fix - will collect bugs and provide new release tonight.

Am Di., 17. Sept. 2019 um 17:48 Uhr schrieb qwang-big < notifications@github.com>:

Hi Michael, here is what I got when providing a lower-case reference fasta

java.lang.IllegalArgumentException: Byte 99 unknown at lib.util.Base.valueOf(Base.java:71) at lib.data.storage.container.FileReferenceProvider.getReferenceBase(FileReferenceProvider.java:90) at lib.data.storage.container.FileReferenceProvider.getReferenceBase(FileReferenceProvider.java:68) at lib.data.assembler.DataAssembler.createDefaultDataContainer(DataAssembler.java:50) at lib.data.assembler.DataAssembler.assembleData(DataAssembler.java:39) at lib.util.ReplicateContainer.getNullDataContainer(ReplicateContainer.java:61) at lib.util.ConditionContainer.getNullDataContainer(ConditionContainer.java:42) at jacusa.worker.CallWorker.createParallelData(CallWorker.java:41)...

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