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
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