Picard SamToFastq error

Question

[NGS-Newbie]

I am trying to convert a sam file to fastq file using picard, but couldn't get the output file - It says it's done but the output file has 0 bytes. Here's is the detailed output. Please suggest if I could use any other program. Thank you all!

$ java -Xmx2048m -jar picard.jar SamToFastq I=F11_R1.sam FASTQ=F11_R1.fastq

picard.sam.SamToFastq INPUT=LF11_R1.sam FASTQ=LF11_R1.fastq OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false 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 Executing as User1@macbook on Mac OS X 10.11.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Picard version: 2.9.0-1-gf5b9f50-SNAPSHOT picard.sam.SamToFastq done. Elapsed time: 3.40 minutes. Runtime.totalMemory()=1084751872 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.lang.String.<init>(String.java:325) at htsjdk.samtools.util.StringUtil.bytesToString(StringUtil.java:301) at htsjdk.samtools.util.StringUtil.bytesToString(StringUtil.java:288) at htsjdk.samtools.BinaryTagCodec.readNullTerminatedString(BinaryTagCodec.java:423) at htsjdk.samtools.BinaryTagCodec.readSingleValue(BinaryTagCodec.java:318) at htsjdk.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:282) at htsjdk.samtools.BAMRecord.decodeAttributes(BAMRecord.java:313) at htsjdk.samtools.BAMRecord.getAttribute(BAMRecord.java:293) at htsjdk.samtools.SAMRecord.isValid(SAMRecord.java:2004) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:795) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:781) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:751) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:569) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:543) at picard.sam.SamToFastq.doWork(SamToFastq.java:174) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)

[NGS-Newbie]

Worked! Thanks, Santosh!

[WouterDeCoster]

Please use ADD COMMENT to reply to earlier reactions. As such this thread remains logically structured and easy to follow. I have now moved your comment, but as you can see it's not optimal.

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Answer 1

[Santosh Anand]

You hit an out-of-memory error. Increase the memory according to what you have -Xmx2048m means maximum 2048megabytes for the JAVA JVM. Make it 70-80% of your max-available memory.