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Picard IlluminaBasecallsToSam error

I'm getting an error when trying to run IlluminaBasecallsToSam. Please help.

java -Xmx8g -jar picard.jar IlluminaBasecallsToSam BASECALLS_DIR=/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls BARCODES_DIR=/project/JIY3012/work/dual_index_umi/250T8B9M8B250T LANE=1 READ_STRUCTURE=250T8B9M8B250T RUN_BARCODE=180619_M00831_0315_000000000-BTMY3 LIBRARY_PARAMS=JIY3012_library_params.xls TMP_DIR=java_io_tmpdir MOLECULAR_INDEX_TAG=RX NUM_PROCESSORS=10 IGNORE_UNEXPECTED_BARCODES=true

17:58:32.040 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/rosema1/BioInfo/bin/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Jun 25 17:58:32 EDT 2018] IlluminaBasecallsToSam BASECALLS_DIR=/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls BARCODES_DIR=/project/JIY3012/work/dual_index_umi/250T8B9M8B250T LANE=1 RUN_BARCODE=180619_M00831_0315_000000000-BTMY3 READ_STRUCTURE=250T8B9M8B250T LIBRARY_PARAMS=JIY3012_library_params.xls NUM_PROCESSORS=10 IGNORE_UNEXPECTED_BARCODES=true MOLECULAR_INDEX_TAG=RX TMP_DIR=[java_io_tmpdir] SEQUENCING_CENTER=BI PLATFORM=illumina ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Mon Jun 25 17:58:32 EDT 2018] Executing as [email protected]_server on Linux 2.6.32-279.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_60-b27; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.7-SNAPSHOT INFO 2018-06-25 17:58:38 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 250T8B9M8B250T Exception in thread "pool-2-thread-7" ERROR 2018-06-25 17:58:39 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:502) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator.awaitWorkComplete(IlluminaBasecallsConverter.java:609) at picard.illumina.IlluminaBasecallsConverter.doTileProcessing(IlluminaBasecallsConverter.java:234) at picard.illumina.IlluminaBasecallsToSam.doWork(IlluminaBasecallsToSam.java:273) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C200.1/s_1_1107.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C200.1/s_1_1107.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more Exception in thread "pool-2-thread-10" picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C200.1/s_1_1110.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C200.1/s_1_1110.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more [Mon Jun 25 17:58:39 EDT 2018] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=1519386624 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.util.RuntimeIOException at htsjdk.samtools.util.BinaryCodec.close(BinaryCodec.java:625) at htsjdk.samtools.BAMFileWriter.finish(BAMFileWriter.java:154) at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:231) at picard.illumina.IlluminaBasecallsToSam$SAMFileWriterWrapper.close(IlluminaBasecallsToSam.java:566) at picard.illumina.IlluminaBasecallsConverter.doTileProcessing(IlluminaBasecallsConverter.java:257) at picard.illumina.IlluminaBasecallsToSam.doWork(IlluminaBasecallsToSam.java:273) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) Caused by: java.nio.channels.ClosedByInterruptException at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202) at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:216) at java.nio.channels.Channels.writeFullyImpl(Channels.java:78) at java.nio.channels.Channels.writeFully(Channels.java:101) at java.nio.channels.Channels.access$000(Channels.java:61) at java.nio.channels.Channels$1.write(Channels.java:174) at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82) at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140) at htsjdk.samtools.util.BlockCompressedOutputStream.flush(BlockCompressedOutputStream.java:267) at htsjdk.samtools.util.BinaryCodec.close(BinaryCodec.java:610) ... 8 more Exception in thread "pool-2-thread-6" Exception in thread "pool-2-thread-11" picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C200.1/s_1_1106.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C200.1/s_1_1106.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C1.1/s_1_1111.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C1.1/s_1_1111.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more Exception in thread "pool-2-thread-5" Exception in thread "pool-2-thread-12" picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C199.1/s_1_1105.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C199.1/s_1_1105.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C2.1/s_1_1112.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C2.1/s_1_1112.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more Exception in thread "pool-2-thread-9" picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C202.1/s_1_1109.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C202.1/s_1_1109.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more Exception in thread "pool-2-thread-2" picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C204.1/s_1_1102.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C204.1/s_1_1102.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more Exception in thread "pool-2-thread-1" picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C198.1/s_1_1101.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C198.1/s_1_1101.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more Exception in thread "pool-2-thread-4" picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C201.1/s_1_1104.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C201.1/s_1_1104.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more Exception in thread "pool-2-thread-3" picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C197.1/s_1_1103.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C197.1/s_1_1103.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more Exception in thread "pool-2-thread-8" picard.PicardException: File not found: (/scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C195.1/s_1_1108.bcl) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:84) at picard.illumina.parser.readers.BclReader.<init>(BclReader.java:94) at picard.illumina.parser.BclParser$BclDataCycleFileParser.<init>(BclParser.java:269) at picard.illumina.parser.BclParser.makeCycleFileParser(BclParser.java:75) at picard.illumina.parser.PerTileCycleParser.makeCycleFileParser(PerTileCycleParser.java:97) at picard.illumina.parser.PerTileCycleParser.seekToTile(PerTileCycleParser.java:133) at picard.illumina.parser.BclParser.initialize(BclParser.java:80) at picard.illumina.parser.BclParser.<init>(BclParser.java:63) at picard.illumina.parser.IlluminaDataProviderFactory.makeParser(IlluminaDataProviderFactory.java:408) at picard.illumina.parser.IlluminaDataProviderFactory.makeDataProvider(IlluminaDataProviderFactory.java:292) at picard.illumina.IlluminaBasecallsConverter$TileReader.process(IlluminaBasecallsConverter.java:463) at picard.illumina.IlluminaBasecallsConverter$TileReadAggregator$1.run(IlluminaBasecallsConverter.java:560) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.FileNotFoundException: /scratch-large/4-quarterly/JIY3012/180619_M00831_0315_000000000-BTMY3/Data/Intensities/BaseCalls/L001/C195.1/s_1_1108.bcl (Too many open files) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at picard.illumina.parser.readers.BaseBclReader.open(BaseBclReader.java:81) ... 14 more 4.83user 3.15system 0:08.53elapsed 93%CPU (0avgtext+0avgdata 2424688maxresident)k 9888inputs+1368outputs (1major+27369minor)pagefaults 0swaps

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