SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Error with MarkDuplicates in Picard slowsmile Bioinformatics 13 11-01-2015 03:16 AM
picard error seq_GA Bioinformatics 2 07-15-2014 04:50 AM
error in picard (SAM validation error) dongshenglulv Bioinformatics 3 07-05-2013 12:58 PM
Picard error JohnK Bioinformatics 14 12-14-2012 05:41 AM
What exactly is AddOrReplaceReadGroups (picard tools) doing? ocs Bioinformatics 6 06-09-2011 07:51 AM

Reply
 
Thread Tools
Old 03-25-2011, 11:48 AM   #1
ercfrtz
Member
 
Location: Iowa

Join Date: Aug 2010
Posts: 23
Default Picard AddOrReplaceReadGroups Error

Hello all,

I am getting the following error when I try to run the AddOrReplaceReadGroups function on picard.


net.sf.picard.sam.AddOrReplaceReadGroups INPUT=/storage/isu/reecy_lab/tmp_eric/9111.1.12.bwa.sorted.bam OUTPUT=/storage/isu/reecy_lab/tmp_eric/9111.1.12.bwa.sorted.corrected.bam SORT_ORDER=coordinate RGLB=BWA RGPL=illumina RGPU=run RGSM=9111 RGID=1 TMP_DIR=/tmp/ercfrtz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
INFO 2011-03-25 14:33:23 AddOrReplaceReadGroups Created read group ID=1 PL=illumina LB=BWA SM=9111

[Fri Mar 25 14:36:18 CDT 2011] net.sf.picard.sam.AddOrReplaceReadGroups done.
Runtime.totalMemory()=922746880
Exception in thread "main" net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; streamed file (filename not available)
at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:199)
at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:189)
at net.sf.samtools.util.BinaryCodec.writeString(BinaryCodec.java:296)
at net.sf.samtools.util.BinaryCodec.writeString(BinaryCodec.java:283)
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:128)
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:37)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:185)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:140)
at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:157)
at net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:93)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117)
at net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:61)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(Unknown Source)
at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
at java.io.BufferedOutputStream.write(Unknown Source)
at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:197)
... 12 more


Any suggestions?
ercfrtz is offline   Reply With Quote
Old 03-28-2011, 05:21 AM   #2
Bruins
Member
 
Location: Groningen

Join Date: Feb 2010
Posts: 78
Default

Carefully read your stack trace:
Quote:
Originally Posted by ercfrtz View Post
[Fri Mar 25 14:36:18 CDT 2011] net.sf.picard.sam.AddOrReplaceReadGroups done.
Runtime.totalMemory()=922746880
Exception in thread "main" net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; streamed file (filename not available)
at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:199)
at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:189)
at net.sf.samtools.util.BinaryCodec.writeString(BinaryCodec.java:296)
at net.sf.samtools.util.BinaryCodec.writeString(BinaryCodec.java:283)
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:128)
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:37)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:185)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:140)
at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:157)
at net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:93)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117)
at net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:61)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(Unknown Source)
at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
at java.io.BufferedOutputStream.write(Unknown Source)
at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:197)
... 12 more
If the problem isn't the dir you're writing in, use an alternative temp dir (in stead of the default /tmp) with sufficient space (check Picard manual).
Bruins is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO