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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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Error making vcfrenamesamples #23

Closed aslett1 closed 9 years ago

aslett1 commented 9 years ago

Hi,

We're getting errors making vcfrenamesamples on our cluster. Full make stack below:

maa@pcs5a:/nfs/pathogen004/maa/jvarkit$ make vcfrenamesamples
mkdir -p /nfs/pathogen004/maa/jvarkit/
rm -rf /nfs/pathogen004/maa/jvarkit/1.128.zip /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/ 
echo "Downloading HTSJDK 1.128 with curl"
Downloading HTSJDK 1.128 with curl
curl  -x "webcache.sanger.ac.uk:3128" -o /nfs/pathogen004/maa/jvarkit/1.128.zip -L "https://github.com/samtools/htsjdk/archive/1.128.zip"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   119    0   119    0     0    316      0 --:--:-- --:--:-- --:--:--   318
100 9326k    0 9326k    0     0  4031k      0 --:--:--  0:00:02 --:--:-- 9206k
unzip /nfs/pathogen004/maa/jvarkit/1.128.zip -d /nfs/pathogen004/maa/jvarkit/
Archive:  /nfs/pathogen004/maa/jvarkit/1.128.zip
429f2a8585d9c98a3efd4cedc5188b60b1e66ac5
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/.classpath  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/.gitignore  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/.project  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/.travis.yml  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/README.md  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/etc/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/etc/test/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/etc/test/junit-noframes.xsl  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/etc/test/testng.css  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/examplestore  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/htsjdk.iml  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/htsjdk.ipr  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/commons-jexl-2.1.1.jar  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/commons-logging-1.1.1.jar  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/jni/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/jni/libIntelDeflater.so  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/snappy-java-1.0.3-rc3.jar  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/testng/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/lib/testng/testng-5.5-jdk15.jar  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/pom.xml  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/c/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/c/inteldeflater/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/c/inteldeflater/IntelDeflater.c  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/AbstractBAMFileIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/AbstractSAMHeaderRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/AlignmentBlock.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/AsyncSAMFileWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMFileConstants.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMFileReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMFileWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMIndexContent.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMIndexMetaData.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMIndexWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMIndexer.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BAMRecordCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BamFileIoUtils.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BamIndexValidator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/Bin.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinList.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinaryBAMIndexWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinaryCigarCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinaryTagCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinningIndexBuilder.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BinningIndexContent.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/BrowseableBAMIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CRAMFileReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CRAMFileWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CRAMIndexer.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CRAMIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CachingBAMFileIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/Chunk.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/Cigar.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CigarElement.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CigarOperator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/ComparableSamRecordIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/CustomReaderFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/DefaultSAMRecordFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/Defaults.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/DiskBasedBAMFileIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/DuplicateScoringStrategy.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/FileTruncatedException.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/FixBAMFile.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/GenomicIndexUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/LinearIndex.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/MergingSamRecordIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/NotPrimarySkippingIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/QueryInterval.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/ReservedTagConstants.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMBinaryTagAndValue.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMException.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileHeader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileSource.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileSpan.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileTruncatedReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileWriterFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFileWriterImpl.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMFormatException.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMHeaderRecordComparator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMLineParser.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMProgramRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMReadGroupRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordComparator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordCoordinateComparator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordQueryNameComparator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordSetBuilder.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMRecordUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMSequenceDictionary.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMSequenceRecord.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMSortOrderChecker.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTag.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTagUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTestUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTextHeaderCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTextReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTextWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMTools.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMUtils.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SAMValidationError.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SQTagUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamFileHeaderMerger.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamFileValidator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamFiles.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamInputResource.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamPairUtil.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamReader.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamReaderFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SamStreams.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/StreamInflatingIndexingOutputStream.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/TagValueAndUnsignedArrayFlag.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/TextCigarCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/TextTagCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/TextualBAMIndexWriter.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/ValidationStringency.java  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/apps/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/apps/TimeChannel.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/apps/TimeRandomAccessFile.java  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/ContainerFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/ContainerParser.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/Cram2SamRecordFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/CramBuilder.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/CramIO.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/CramNormalizer.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/Sam2CramRecordFactory.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/build/Utils.java  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/CramVersions.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/IntHashMap.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/MutableInt.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/NonforgivingPrintStream.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/NullOutputStream.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/common/Version.java  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/encoding/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/encoding/AbstractBitCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/encoding/ArithCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/encoding/ArithCodec1.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/encoding/BetaIntegerCodec.java  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/encoding/BetaIntegerEncoding.java  
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 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/compressed.sam.gz  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/coordinate_sorted.sam  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/empty.bai  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/empty.bam  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/empty_no_empty_gzip_block.bai  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/empty_no_empty_gzip_block.bam  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/intervallist/
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  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestCompInverseManual.interval_list  
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  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManualComp.interval_list  
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/io/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/io/5newline5.txt  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/io/empty.txt  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/io/slurptest.txt  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/issue76.bam  
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/liftover/
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/reference/
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  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.noindex.fasta  
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/util/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/util/QualityEncodingDetectorTest/
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 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/util/QualityEncodingDetectorTest/illumina-as-standard.bam  
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 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/util/defective_bgzf.bam  
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/samtools/util/no_bgzf_terminator.bam  
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/tribble/tmp/
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/htsjdk/variant/utils/SamSequenceDictionaryExtractor/
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C1.1/
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C10.1/
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C11.1/
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   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C12.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C13.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C14.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C15.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C16.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C17.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C18.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C19.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C2.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C20.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C21.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C22.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C23.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C24.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C25.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C26.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C27.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C28.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C29.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C3.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C30.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C31.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C32.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C33.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C34.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C35.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C36.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C37.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C38.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C39.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C4.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C40.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C41.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C42.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C43.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C44.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C45.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C46.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C47.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C48.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C49.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C5.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C50.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C51.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C52.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C53.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C54.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C55.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C56.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C57.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C58.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C59.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C6.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C60.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C61.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C62.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C63.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C64.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C65.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C66.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C7.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C8.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C9.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/s_1_1101.filter  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/L001/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/125T125T/Data/Intensities/L001/s_1_1101.clocs  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C10.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C11.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C12.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C13.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C14.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C15.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C16.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C17.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C18.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C19.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C2.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C20.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C21.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C22.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C23.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C24.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C25.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/N.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam  
  inflating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/net/sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam  
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/tribble/
   creating: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/tribble/tmp/
 extracting: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testdata/tribble/tmp/.gitignore  
find /nfs/pathogen004/maa/jvarkit/htsjdk-1.128 -exec touch '{}'  ';'
rm -f /nfs/pathogen004/maa/jvarkit/1.128.zip
echo "Compiling htsjdk with ${JAVA_HOME} = /software/pathogen/external/apps/usr/local/jdk1.7.0_21/"
Compiling htsjdk with /software/pathogen/external/apps/usr/local/jdk1.7.0_21/ = /software/pathogen/external/apps/usr/local/jdk1.7.0_21/
echo "Compiling htsjdk library for java. Requires  apache ANT. If it fails here, it's a not a problem with jvarkit."
Compiling htsjdk library for java. Requires  apache ANT. If it fails here, it's a not a problem with jvarkit.
(cd /nfs/pathogen004/maa/jvarkit/htsjdk-1.128 && ant )
Buildfile: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml

write-version-property:
[propertyfile] Creating new property file: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/htsjdk.version.properties

init:

compile-samtools:
    [mkdir] Created dir: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/classes
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:244: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 371 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/io/ByteBufferUtils.java:360: warning: CRC16 is internal proprietary API and may be removed in a future release
    [javac]         sun.misc.CRC16 crc16 = new sun.misc.CRC16();
    [javac]                 ^
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/samtools/cram/io/ByteBufferUtils.java:360: warning: CRC16 is internal proprietary API and may be removed in a future release
    [javac]         sun.misc.CRC16 crc16 = new sun.misc.CRC16();
    [javac]                                            ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 3 warnings

compile-tribble:
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:244: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 72 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-variant:
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:244: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 61 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] Note: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/java/htsjdk/variant/vcf/AbstractVCFCodec.java uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-src:

compile-samtools-tests:
    [mkdir] Created dir: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testclasses
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:265: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 67 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testclasses
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-tribble-tests:
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:265: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 23 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testclasses
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-variant-tests:
    [javac] /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/build.xml:265: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 20 source files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/testclasses
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6
    [javac] Note: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/src/tests/java/htsjdk/variant/variantcontext/GenotypeLikelihoodsUnitTest.java uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 warning

compile-tests:

compile:

htsjdk-jar:
    [mkdir] Created dir: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist
      [jar] Building jar: /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/htsjdk-1.128.jar
     [copy] Copying 3 files to /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist

all:

BUILD SUCCESSFUL
Total time: 25 seconds
touch --no-create /nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/commons-jexl-2.1.1.jar
mkdir -p /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/
echo "package com.github.lindenb.jvarkit.util.htsjdk;" > /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo '@javax.annotation.Generated("jvarkit")' >> /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public class HtsjdkVersion{ private HtsjdkVersion(){}' >> /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getVersion() {return "1.128";}' >> /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getHome() {return "/nfs/pathogen004/maa/jvarkit/htsjdk-1.128";}' >> /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo '}'  >> /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo "### COMPILING vcfrenamesamples ######"
### COMPILING vcfrenamesamples ######
mkdir -p /nfs/pathogen004/maa/jvarkit/_tmp-1.128/META-INF /nfs/pathogen004/maa/jvarkit/dist-1.128 galaxy-bundle/jvarkit
#create galaxy
rm -f galaxy-bundle/vcfrenamesamples.xml
xsltproc --path /nfs/pathogen004/maa/jvarkit/src/main/resources/xml --output galaxy-bundle/jvarkit/vcfrenamesamples.xml --stringparam name "vcfrenamesamples" --stringparam class "com.github.lindenb.jvarkit.tools.misc.VcfRenameSamples" --stringparam classpath "commons-jexl-2.1.1.jar commons-logging-1.1.1.jar htsjdk-1.128.jar snappy-java-1.0.3-rc3.jar vcfrenamesamples.jar" --stringparam version  `cat  /nfs/pathogen004/maa/jvarkit/.git/refs/heads/master ` /nfs/pathogen004/maa/jvarkit/src/main/resources/xsl/tools2galaxy.xsl /nfs/pathogen004/maa/jvarkit/src/main/resources/xml/tools.xml || echo "XSLT failed (ignored)"
XSLT failed (ignored)
cp galaxy-bundle/jvarkit/vcfrenamesamples.xml /nfs/pathogen004/maa/jvarkit/_tmp-1.128/META-INF/galaxy.xml 
cp: cannot stat `galaxy-bundle/jvarkit/vcfrenamesamples.xml': No such file or directory
make: [vcfrenamesamples] Error 1 (ignored)
#copy resource
cp /nfs/pathogen004/maa/jvarkit/src/main/resources/messages/messages.properties /nfs/pathogen004/maa/jvarkit/_tmp-1.128
#compile
javac -d /nfs/pathogen004/maa/jvarkit/_tmp-1.128 -g -classpath "/nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/commons-jexl-2.1.1.jar:/nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/commons-logging-1.1.1.jar:/nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/htsjdk-1.128.jar:/nfs/pathogen004/maa/jvarkit/htsjdk-1.128/dist/snappy-java-1.0.3-rc3.jar" -sourcepath /nfs/pathogen004/maa/jvarkit/src/main/java:/nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java /nfs/pathogen004/maa/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java /nfs/pathogen004/maa/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfRenameSamples.java
/nfs/pathogen004/maa/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:268: illegal start of type
        LinkedHashSet<String> vcfFiles= new LinkedHashSet<>(inputs.size()+1);
                                                          ^
/nfs/pathogen004/maa/jvarkit/src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java:171: cannot find symbol
symbol  : constructor GZIPOutputStream(java.io.FileOutputStream,boolean)
location: class java.util.zip.GZIPOutputStream
            return new GZIPOutputStream(new FileOutputStream(file),true);
                   ^
2 errors
make: *** [vcfrenamesamples] Error 1
lindenb commented 9 years ago

Your version of java is NOT the right one = (NOT 1.7) . Please check your PATH.

The diamond notation

LinkedHashSet<> ...

is only supported in java 1.7 see 'Diamond' in http://docs.oracle.com/javase/tutorial/java/generics/types.html

And you can see at http://docs.oracle.com/javase/7/docs/api/java/util/zip/GZIPOutputStream.html#GZIPOutputStream%28java.io.OutputStream,%20boolean%29

the constructor GZIPOutputStream(file,boolean) was created for java 1.7

aslett1 commented 9 years ago

Ah, that's annoying. We'd set $JAVA_HOME to point to 1.7 but the path version still defaults to 1.6.

lindenb commented 9 years ago

try 

export PATH=${JAVA_HOME}/bin:${PATH}
aslett1 commented 9 years ago

I've done exactly that and it works fine. Thanks!!

On Tue, 17 Mar 2015, Pierre Lindenbaum wrote:

try

export PATH=${JAVA_HOME}/bin:${PATH}

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