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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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COBALT error #85

Closed hastj7373 closed 4 years ago

hastj7373 commented 4 years ago

Hello.

Could you please tell me how to fix the problem below? (AMBER worked for me, but COBALT didn't work..)

16:49:38 - COBALT version: 1.8 16:49:38 - Thread Count: 4, Window Size: 1000, Min Quality 10 16:49:38 - Reading GC Profile 16:49:38 - Complete Exception in thread "main" java.io.UncheckedIOException: java.nio.charset.MalformedInputException: Input length = 1 at java.io.BufferedReader$1.hasNext(BufferedReader.java:574) at java.util.Iterator.forEachRemaining(Iterator.java:115) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566) at com.hartwig.hmftools.common.utils.io.reader.LineReader.read(LineReader.java:38) at com.hartwig.hmftools.common.utils.io.reader.LineReader.lambda$build$0(LineReader.java:25) at com.hartwig.hmftools.common.genome.gc.GCProfileFactory.loadGCContent(GCProfileFactory.java:29) at com.hartwig.hmftools.cobalt.CountBamLinesApplication.run(CountBamLinesApplication.java:86) at com.hartwig.hmftools.cobalt.CountBamLinesApplication.main(CountBamLinesApplication.java:46) Caused by: java.nio.charset.MalformedInputException: Input length = 1 at java.nio.charset.CoderResult.throwException(CoderResult.java:281) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:339) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at java.io.BufferedReader$1.hasNext(BufferedReader.java:571) ... 12 more

alhafidzhamdan commented 4 years ago

Hi did you actually manage to resolve the issue @hastj7373 ? I am encountering the same issue. Would be good if anyone on here could help? probably a very simple issue.

lkhilton commented 4 years ago

@alhafidzhamdan you have to make sure the gc profile you download from the hmftools resources are unzipped.