Oh thanks. I did use ExtractIlluminaBarcodes. Could this be something wrong with my barcodeData file used for the extraction? I can try recreating the file and running ExtractIlluminaBarcodes again.
On May 29, 2014, at 11:42 AM, Alec Wysoker <[email protected]> wrote: > Hi Stephen, > > There is a problem with your *_barcode.txt files. In some of the lines, > there is a space character after the second barcode (the one in column 3). > Were these created with ExtractIlluminaBarcodes, or did you use some other > process, or did they get modified after creating with ExtractIlluminaBarcodes? > > The immediate solution is to remove all those space characters, but if there > is a bug in ExtractIlluminaBarcodes I would like to know it. > > -Alec > > On May 28, 2014, at 4:11 PM, Gire, Stephen <[email protected]> wrote: > >> I am demultiplexing a TruSeq small RNA run using 6 cycle barcodes. I am able >> to Extract the Illumina barcodes into metrics.txt and they look fine. >> However, when I try to convert the raw files to .bams using the >> IlluminaBasecallsToSam.jar I keep getting several errors. I’ve used this >> script with 8 cycle barcodes with no problem. >> >> The first error states that there was an unexpected number of elements when >> parsing file s_2_1102_barcode.txt. It says the expected maximum of elements >> per line is 5, which there are no more than 5, so I am a bit confused. >> >> Any help would be appreciated. I’ve never seen this error before and I’m >> wondering if it’s a specific issue with smallRNA pipelines? >> >> Thanks. >> >> Log Report: >> >> Your job looked like: >> >> ------------------------------------------------------------ >> # LSBATCH: User input >> java -Xmx10g -jar >> /seq/software/picard/current/bin/IlluminaBasecallsToSam.jar >> BASECALLS_DIR=/broad/hptmp/SGire/20140522.140114_SL-HDC_0407_AFCH7576ADXX/Data/Intensities/BaseCalls/ >> LANE=2 READ_STRUCTURE=125T6B125T >> LIBRARY_PARAMS=/idi/sabeti-data/SGire/EBOV_miRNA/library_params.txt >> SEQUENCING_CENTER=Broad RUN_BARCODE=140114_SL-HDC_0407_AFCH7576ADXX >> NUM_PROCESSORS=4 ADAPTERS_TO_CHECK=TRUSEQ_SMALLRNA >> MAX_READS_IN_RAM_PER_TILE=100000 MAX_RECORDS_IN_RAM=100000 FORCE_GC=false >> ------------------------------------------------------------ >> >> Exited with exit code 1. >> >> Resource usage summary: >> >> CPU time : 9.87 sec. >> Max Memory : 191 MB >> Max Swap : 10591 MB >> >> Max Processes : 3 >> Max Threads : 25 >> >> The output (if any) follows: >> >> [Wed May 28 15:28:39 EDT 2014] picard.illumina.IlluminaBasecallsToSam >> BASECALLS_DIR=/broad/hptmp/SGire/20140522.140114_SL-HDC_0407_AFCH7576ADXX/Data/Intensities/BaseCalls >> LANE=2 RUN_BARCODE=140114_SL-HDC_0407_AFCH7576ADXX SEQUENCING_CENTER=Broad >> READ_STRUCTURE=125T6B125T >> LIBRARY_PARAMS=/idi/sabeti-data/SGire/EBOV_miRNA/library_params.txt >> ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM, >> TRUSEQ_SMALLRNA] NUM_PROCESSORS=4 FORCE_GC=false >> MAX_READS_IN_RAM_PER_TILE=100000 MAX_RECORDS_IN_RAM=100000 >> PLATFORM=illumina APPLY_EAMSS_FILTER=true MINIMUM_QUALITY=2 >> INCLUDE_NON_PF_READS=true VERBOSITY=INFO QUIET=false >> VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false >> CREATE_MD5_FILE=false >> [Wed May 28 15:28:39 EDT 2014] Executing as sgire@node1005 on Linux >> 2.6.18-194.8.1.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_35-b10; >> Picard version: 1.727(06603b8dd6204c5d29e2c4e28a55bef15a7324d1_1400679360) >> JdkDeflater >> INFO 2014-05-28 15:30:24 IlluminaBasecallsToSam DONE_READING STRUCTURE >> IS 125T6B125T >> ERROR Exception in thread "pool-1-thread-2" picard.PicardException: >> Unexpected number of elements found when parsing file >> /broad/hptmp/SGire/20140522.140114_SL-HDC_0407_AFCH7576ADXX/Data/Intensities/BaseCalls/s_2_1102_barcode.txt: >> 5. Expected a maximum of 5 elements per line:TTAGGC Y TTAGGC 0 >> 3 >> at >> picard.util.AbstractInputParser.parseLine(AbstractInputParser.java:129) >> at picard.util.AbstractInputParser.advance(AbstractInputParser.java:88) >> at picard.util.AbstractInputParser.advance(AbstractInputParser.java:44) >> at htsjdk.samtools.util.AbstractIterator.next(AbstractIterator.java:57) >> at >> picard.illumina.parser.readers.BarcodeFileReader.next(BarcodeFileReader.java:29) >> at >> picard.illumina.parser.BarcodeParser$BarcodeDataIterator$1.getBarcode(BarcodeParser.java:75) >> at >> picard.illumina.parser.IlluminaDataProvider.addData(IlluminaDataProvider.java:178) >> at >> picard.illumina.parser.IlluminaDataProvider.next(IlluminaDataProvider.java:145) >> at >> picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:499) >> at >> picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$2.run(IlluminaBasecallsConverter.java:601) >> at >> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) >> at >> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) >> at java.lang.Thread.run(Thread.java:662) >> 2014-05-28 15:30:45 IlluminaBasecallsConverter Failure encountered in >> worker thread; attempting to shut down remaining worker threads and >> terminate ... >> java.lang.InterruptedException >> at java.lang.Object.wait(Native Method) >> at java.lang.Object.wait(Object.java:485) >> at >> picard.illumina.IlluminaBasecallsConverter$TileReadAggregator.awaitWorkComplete(IlluminaBasecallsConverter.java:653) >> at >> picard.illumina.IlluminaBasecallsConverter.doTileProcessing(IlluminaBasecallsConverter.java:269) >> at >> picard.illumina.IlluminaBasecallsToSam.doWork(IlluminaBasecallsToSam.java:205) >> at >> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183) >> at >> picard.illumina.IlluminaBasecallsToSam.main(IlluminaBasecallsToSam.java:411) >> WARNING 2014-05-28 15:30:45 IlluminaBasecallsConverter >> Ignoring exception stopping background GC thread. >> java.lang.NullPointerException >> at >> picard.illumina.IlluminaBasecallsConverter.doTileProcessing(IlluminaBasecallsConverter.java:284) >> at >> picard.illumina.IlluminaBasecallsToSam.doWork(IlluminaBasecallsToSam.java:205) >> at >> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183) >> at >> picard.illumina.IlluminaBasecallsToSam.main(IlluminaBasecallsToSam.java:411) >> Exception in thread "pool-1-thread-1" picard.PicardException: IOException >> opening cluster binary file >> /broad/hptmp/SGire/20140522.140114_SL-HDC_0407_AFCH7576ADXX/Data/Intensities/BaseCalls/L002/s_2_1101.filter >> at >> picard.illumina.parser.readers.MMapBackedIteratorFactory.getBuffer(MMapBackedIteratorFactory.java:119) >> at >> picard.illumina.parser.readers.MMapBackedIteratorFactory.getByteIterator(MMapBackedIteratorFactory.java:66) >> at >> picard.illumina.parser.readers.FilterFileReader.<init>(FilterFileReader.java:68) >> at picard.illumina.parser.FilterParser$1.<init>(FilterParser.java:55) >> at >> picard.illumina.parser.FilterParser.makeTileIterator(FilterParser.java:54) >> at >> picard.illumina.parser.PerTileParser.advanceTile(PerTileParser.java:80) >> at picard.illumina.parser.PerTileParser.hasNext(PerTileParser.java:121) >> at >> picard.illumina.parser.PerTileParser.maybeAdvance(PerTileParser.java:99) >> at picard.illumina.parser.PerTileParser.next(PerTileParser.java:109) >> at >> picard.illumina.parser.IlluminaDataProvider.next(IlluminaDataProvider.java:133) >> at >> picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:499) >> at >> picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$2.run(IlluminaBasecallsConverter.java:601) >> at >> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) >> at >> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) >> at java.lang.Thread.run(Thread.java:662) >> Caused by: java.nio.channels.ClosedByInterruptException >> at >> java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:184) >> at sun.nio.ch.FileChannelImpl.size(FileChannelImpl.java:304) >> at >> picard.illumina.parser.readers.MMapBackedIteratorFactory.getBuffer(MMapBackedIteratorFactory.java:113) >> ... 14 more >> Exception in thread "pool-1-thread-3" picard.PicardException: IOException >> opening cluster binary file >> /broad/hptmp/SGire/20140522.140114_SL-HDC_0407_AFCH7576ADXX/Data/Intensities/BaseCalls/L002/s_2_1103.filter >> at >> picard.illumina.parser.readers.MMapBackedIteratorFactory.getBuffer(MMapBackedIteratorFactory.java:119) >> at >> picard.illumina.parser.readers.MMapBackedIteratorFactory.getByteIterator(MMapBackedIteratorFactory.java:66) >> at >> picard.illumina.parser.readers.FilterFileReader.<init>(FilterFileReader.java:68) >> at picard.illumina.parser.FilterParser$1.<init>(FilterParser.java:55) >> at >> picard.illumina.parser.FilterParser.makeTileIterator(FilterParser.java:54) >> at >> picard.illumina.parser.PerTileParser.advanceTile(PerTileParser.java:80) >> at picard.illumina.parser.PerTileParser.hasNext(PerTileParser.java:121) >> at >> picard.illumina.parser.IlluminaDataProvider.hasNext(IlluminaDataProvider.java:104) >> at >> picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:498) >> at >> picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$2.run(IlluminaBasecallsConverter.java:601) >> at >> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) >> at >> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) >> at java.lang.Thread.run(Thread.java:662) >> Caused by: java.nio.channels.ClosedByInterruptException >> at >> java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:184) >> at sun.nio.ch.FileChannelImpl.size(FileChannelImpl.java:304) >> at >> picard.illumina.parser.readers.MMapBackedIteratorFactory.getBuffer(MMapBackedIteratorFactory.java:113) >> ... 12 more >> [Wed May 28 15:30:45 EDT 2014] picard.illumina.IlluminaBasecallsToSam done. >> Elapsed time: 2.11 minutes. >> Runtime.totalMemory()=367525888 >> To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp >> Exception in thread "main" picard.PicardException: Failure encountered in >> worker thread; see log for details. >> at >> picard.illumina.IlluminaBasecallsConverter.doTileProcessing(IlluminaBasecallsConverter.java:272) >> at >> picard.illumina.IlluminaBasecallsToSam.doWork(IlluminaBasecallsToSam.java:205) >> at >> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183) >> at >> picard.illumina.IlluminaBasecallsToSam.main(IlluminaBasecallsToSam.java:411) >> Exception in thread "pool-1-thread-4" picard.PicardException: IOException >> opening cluster binary file >> /broad/hptmp/SGire/20140522.140114_SL-HDC_0407_AFCH7576ADXX/Data/Intensities/BaseCalls/L002/s_2_1104.filter >> at >> picard.illumina.parser.readers.MMapBackedIteratorFactory.getBuffer(MMapBackedIteratorFactory.java:119) >> at >> picard.illumina.parser.readers.MMapBackedIteratorFactory.getByteIterator(MMapBackedIteratorFactory.java:66) >> at >> picard.illumina.parser.readers.FilterFileReader.<init>(FilterFileReader.java:68) >> at picard.illumina.parser.FilterParser$1.<init>(FilterParser.java:55) >> at >> picard.illumina.parser.FilterParser.makeTileIterator(FilterParser.java:54) >> at >> picard.illumina.parser.PerTileParser.advanceTile(PerTileParser.java:80) >> at picard.illumina.parser.PerTileParser.hasNext(PerTileParser.java:121) >> at >> picard.illumina.parser.PerTileParser.maybeAdvance(PerTileParser.java:99) >> at picard.illumina.parser.PerTileParser.next(PerTileParser.java:109) >> at >> picard.illumina.parser.IlluminaDataProvider.next(IlluminaDataProvider.java:133) >> at >> picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:499) >> at >> picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$2.run(IlluminaBasecallsConverter.java:601) >> at >> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) >> at >> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) >> at java.lang.Thread.run(Thread.java:662) >> Caused by: java.nio.channels.ClosedByInterruptException >> at >> java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:184) >> at sun.nio.ch.FileChannelImpl.size(FileChannelImpl.java:304) >> at >> picard.illumina.parser.readers.MMapBackedIteratorFactory.getBuffer(MMapBackedIteratorFactory.java:113) >> ... 14 more >> ------------------------------------------------------------------------------ >> Time is money. 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