Error while converting FastqToSam

Question

[ChIP]

Hi,

I am trying to convert a fastq file into sam using picard tool utility FastqToSam. I am fiollowing what it says in manual.

The data that I am using is from geo http://www.ncbi.nlm.nih.gov/sra?term=SRX105932 (this is paired end, data submitted in a very different manner) I already converted this SRA into fastq using Fastq-dump

fastq-dump -A SRR364680.sra
fastq-dump -A SRR384964.sra

After this I got two files SRR364680.sra.fastq & SRR384964.sra.fastq, Since the reads in the two files are not in the same order. I wanted to produce an unaligned bams and then merge them followed by sorting and then arranging the paired reads in two files.

But I already stumbled at the first step of FastqToSam

I am using

FastqToSam F1=SRR364680.sra.fastq O=read1.bam SM=sampleName SO=unsorted V=Illumina Validation_STRINGENCY=LENIENT

and the error I get is

[Thu Dec 18 10:04:56 CET 2014] net.sf.picard.sam.FastqToSam FASTQ=SRR364680.sra.fastq QUALITY_FORMAT=Illumina OUTPUT=read1.bam SAMPLE_NAME=sampleName SORT_ORDER=unsorted VALIDATION_STRINGENCY=LENIENT    READ_GROUP_NAME=A MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Dec 18 10:04:56 CET 2014] Executing as arun@06 on Linux 3.12.21-gentoo-r1 amd64; OpenJDK 64-Bit Server VM 1.6.0_31-b31; Picard version: 1.101(Unversioned directory)
[Thu Dec 18 10:04:56 CET 2014] net.sf.picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2058027008
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" net.sf.picard.PicardException: Base quality 227 is not in the range 0..93 for read SRR364680.sra.1 SFGF-GA2-1_63:2:112:1559:999 length=80
    at net.sf.picard.sam.FastqToSam.createSamRecord(FastqToSam.java:222)
    at net.sf.picard.sam.FastqToSam.doUnpaired(FastqToSam.java:158)
    at net.sf.picard.sam.FastqToSam.doWork(FastqToSam.java:140)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
    at net.sf.picard.sam.FastqToSam.main(FastqToSam.java:118)

Does anyone knows, how to fix this?

Thank you

Answer 1

[GouthamAtla]

I can see that this data is from Genome Analyzer II. Leave the V option with default parameters. It will detect the encoding automatically.

[ChIP]

Yes, that is why I have used V=Illumina. Or should I use something else?

[GouthamAtla]

use defaults. or use 'Standard'