In running Picard Tools' AddOrReplaceReadGroups, I got an error that included the following:
This sounds like I have run out of disk space, but I haven't. My command was the following:
I found some threads discussing these problems, but couldn't find a solution there. Can anyone suggest a solution? The full error message is pasted below.
Thank you.
Eric
Code:
Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.IOException: No space left on device
Code:
java -d64 -Xmx25g -jar /home/efoss/source_codes/picard-tools-1.82/AddOrReplaceReadGroups.jar \ INPUT=AML_PAERAH_73407_RNA_partialperlclean_noMT.sam \ OUTPUT=AML_PAERAH_73407_RNA_partialperlclean_noMT_AORRGaddedsorted.sam \ SORT_ORDER=coordinate \ RGID=RGID_PAERAH_73407 \ RGLB=PAERAH_73407_library \ RGPL=Illumina \ RGPU=run_barcode_arbitrary \ RGSM=AML_PAERAH_73407_RNAseq \ RGCN=FHCRC \ RGDS=AML_PAERAH_73407_RNAseq \ RGDT=2012-12-22
Thank you.
Eric
Code:
[efoss@gizmod64:~/sequencing/MAE_in_AML$ java -d64 -Xmx25g -jar /home/efoss/source_codes/picard-tools-1.82/AddOrReplaceReadGroups.jar \ > INPUT=AML_PAERAH_73407_RNA_partialperlclean_noMT.sam \ > OUTPUT=AML_PAERAH_73407_RNA_partialperlclean_noMT_AORRGaddedsorted.sam \ > SORT_ORDER=coordinate \ > RGID=RGID_PAERAH_73407 \ > RGLB=PAERAH_73407_library \ > RGPL=Illumina \ > RGPU=run_barcode_arbitrary \ > RGSM=AML_PAERAH_73407_RNAseq \ > RGCN=FHCRC \ > RGDS=AML_PAERAH_73407_RNAseq \ > RGDT=2012-12-22 [Mon Dec 24 12:29:53 PST 2012] net.sf.picard.sam.AddOrReplaceReadGroups INPUT=AML_PAERAH_73407_RNA_partialperlclean_noMT.sam OUTPUT=AML_PAERAH_73407_RNA_partialperlclean_noMT_AORRGaddedsorted.sam SORT_ORDER=coordinate RGID=RGID_PAERAH_73407 RGLB=PAERAH_73407_library RGPL=Illumina RGPU=run_barcode_arbitrary RGSM=AML_PAERAH_73407_RNAseq RGCN=FHCRC RGDS=AML_PAERAH_73407_RNAseq RGDT=2012-12-21T16:00:00-0800 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Dec 24 12:29:53 PST 2012] Executing as efoss@gizmod64 on Linux 3.2.0-24-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_24-b24; Picard version: 1.82(1311) INFO 2012-12-24 12:29:53 AddOrReplaceReadGroups Created read group ID=RGID_PAERAH_73407 PL=Illumina LB=PAERAH_73407_library SM=AML_PAERAH_73407_RNAseq [Mon Dec 24 12:30:01 PST 2012] net.sf.picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.13 minutes. Runtime.totalMemory()=1910898688 FAQ: [url]http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page[/url] Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.IOException: No space left on device 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.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:100) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) at net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:66) Caused by: java.io.IOException: No space left on device at java.io.FileOutputStream.write(Native Method) at org.xerial.snappy.SnappyOutputStream.writeInt(SnappyOutputStream.java:105) at org.xerial.snappy.SnappyOutputStream.dump(SnappyOutputStream.java:126) at org.xerial.snappy.SnappyOutputStream.flush(SnappyOutputStream.java:100) at org.xerial.snappy.SnappyOutputStream.close(SnappyOutputStream.java:137) at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:219) ... 6 more efoss@gizmod64:~/sequencing/MAE_in_AML$
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