RevertBamToFastq

Revert bam to fastq

Create a working folder mkdir RevertBamToFastq

copy across needed files

fast:

cp ToBePostProcess/Sample_Diag-excap33-13001128402-EEogPU-v01-KIT-Av5/000_fastqFilesAndQC/Diag-excap33-13001128402-EEogPU-v01-KIT-Av5_GCCAAT_L005_R* RevertBamToFastq/

bam:

starting:
cp ToBePostProcess/Sample_Diag-excap33-13001128402-EEogPU-v01-KIT-Av5/mapping_2014-11-10_033730/results/141028_7001448_0280_BC5MRDANXX_Sample_Diag-excap33-13001128402-EEogPU-v01-KIT-Av5_GCCAAT_L005.posiSrt.bam RevertBamToFastq/

final:

cp ToBePostProcess/Sample_Diag-excap33-13001128402-EEogPU-v01-KIT-Av5/060_delivery/all.realigned.markDup.baseQreCali.bam ToBePostProcess/

13/11/2014

From old recipe:

First revert to the original bam with:
java -Xmx8g -jar picard-tools-1.62/RevertSam.jar INPUT=processed.bam OUTPUT=original.bam SORT_ORDER=unsorted RESTORE_ORIGINAL_QUALITIES=true
Second change the format to fastq:
java -Xmx8g -jar picard-tools-1.62/SamToFastq.jar INPUT=original.bam OUTPUT_DIR= OUTPUT_PER_RG=True

Now use the same picard as in the pipeline

picard = /data/diag/diagInternal/diagnosticBundle/tools/picard-tools-1.107/picard-tools-1.107

java -Xmx8g -jar $picard/RevertSam.jar INPUT=all.realigned.markDup.baseQreCali.bam OUTPUT=original.bam SORT_ORDER=unsorted RESTORE_ORIGINAL_QUALITIES=true

INFO	2014-11-13 12:17:13	RevertSam	Reverted   139,000,000 records.  Elapsed time: 01:40:21s.  Time for last 1,000,000:   53s.  Last read position: */*
INFO	2014-11-13 12:18:02	RevertSam	Reverted   140,000,000 records.  Elapsed time: 01:41:10s.  Time for last 1,000,000:   49s.  Last read position: */*
[Thu Nov 13 12:18:22 CET 2014] net.sf.picard.sam.RevertSam done. Elapsed time: 101.52 minutes.
Runtime.totalMemory()=1746403328

java -Xmx8g -jar $picard/SamToFastq.jar INPUT=original.bam OUTPUT_DIR=./  OUTPUT_PER_RG=True

Errors!!!

[Thu Nov 13 16:58:25 CET 2014] net.sf.picard.sam.SamToFastq done. Elapsed time: 264.28 minutes.
Runtime.totalMemory()=4622123008
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
	at java.lang.String.(String.java:315)
	at net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:301)
	at net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:288)
	at net.sf.samtools.BinaryTagCodec.readNullTerminatedString(BinaryTagCodec.java:420)
	at net.sf.samtools.BinaryTagCodec.readSingleValue(BinaryTagCodec.java:318)
	at net.sf.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:282)
	at net.sf.samtools.BAMRecord.decodeAttributes(BAMRecord.java:308)
	at net.sf.samtools.BAMRecord.getAttribute(BAMRecord.java:288)
	at net.sf.samtools.SAMRecord.isValid(SAMRecord.java:1628)
	at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:620)
	at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:606)
	at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:576)
	at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:768)
	at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:746)
	at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:130)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
	at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:118)

yvans@loki:/data/diag/diagInternal/samples/141028_7001448.B.Project_Diag-excap33-2014-10-24/RevertBamToFastq
> java -Xmx8g -jar $picard/SamToFastq.jar INPUT=original.bam OUTPUT_DIR=./  OUTPUT_PER_RG=True MAX_RECORDS_IN_RAM=5000000 2> errsatofastq.txt