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rjeschmi/gist:f4adeeb6a655a059c8de

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gistfile1.txt
[Tue Oct 07 01:24:47 GMT 2014] net.sf.picard.sam.FastqToSam FASTQ=unmapped_left.fastq.gz QUALITY_FORMAT=Standard OUTPUT=unmapped.bam SAMPLE_NAME=560Iplus-Ter119minus READ_GROUP_NAME=A SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false[Tue Oct 07 01:24:47 GMT 2014] Executing as rob@solexa10 on Linux 3.2.63-1.el5.elrepo amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_23-b05; Picard version: 1.78(1278)
[Tue Oct 07 01:24:47 GMT 2014] net.sf.picard.sam.FastqToSam FASTQ=unmapped_left.fastq.gz QUALITY_FORMAT=Standard OUTPUT=unmapped.bam SAMPLE_NAME=Null_Ter119+ READ_GROUP_NAME=A SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue Oct 07 01:24:47 GMT 2014] Executing as rob@solexa10 on Linux 3.2.63-1.el5.elrepo amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_23-b05; Picard version: 1.78(1278)
[Tue Oct 07 01:24:47 GMT 2014] Executing as rob@solexa10 on Linux 3.2.63-1.el5.elrepo amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_23-b05; Picard version: 1.78(1278)
[Tue Oct 07 01:24:47 GMT 2014] Executing as rob@solexa10 on Linux 3.2.63-1.el5.elrepo amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_23-b05; Picard version: 1.78(1278)
[Tue Oct 07 01:24:47 GMT 2014] Executing as rob@solexa10 on Linux 3.2.63-1.el5.elrepo amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_23-b05; Picard version: 1.78(1278)
[Tue Oct 07 01:24:47 GMT 2014] Executing as rob@solexa10 on Linux 3.2.63-1.el5.elrepo amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_23-b05; Picard version: 1.78(1278)[Tue Oct 07 01:24:47 GMT 2014] Executing as rob@solexa10 on Linux 3.2.63-1.el5.elrepo amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_23-b05; Picard version: 1.78(1278)
[Tue Oct 07 01:24:47 GMT 2014] Executing as rob@solexa10 on Linux 3.2.63-1.el5.elrepo amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_23-b05; Picard version: 1.78(1278)
[Tue Oct 07 01:25:09 GMT 2014] net.sf.picard.sam.FastqToSam done. Elapsed time: 0.36 minutes.
Runtime.totalMemory()=2058027008
FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.IOException: No such file or directory
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:228)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:150)
at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:170)
at net.sf.picard.sam.FastqToSam.doUnpaired(FastqToSam.java:143)
at net.sf.picard.sam.FastqToSam.doWork(FastqToSam.java:123)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.sam.FastqToSam.main(FastqToSam.java:118)
Caused by: java.io.IOException: No such file or directory
at java.io.UnixFileSystem.createFileExclusively(Native Method)
at java.io.File.checkAndCreate(Unknown Source)
at java.io.File.createTempFile(Unknown Source)
at net.sf.samtools.util.IOUtil.newTempFile(IOUtil.java:100)
at net.sf.samtools.util.SortingCollection.newTempFile(SortingCollection.java:237)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:204)
... 6 more
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