Fastq to sam issues

[Wallysb01]

So, I've been trying to convert my .fastq files to .sam files in order to use scripture to align the reads without using a reference genome. To do this I've installed picard (along with samtools and the rest of the men's wear suite), however when I try to run the FastqToSam function I get an error I do not understand.

My input:

java -Xmx2g -jar FastqToSam.jar FASTQ=file1.fastq FASTQ2=file2.fastq OUTPUT=file3.sam PREDICTED_INSERT_SIZE=xx QUALITY_FORMAT=Illumina SAMPLE_NAME=file4

and the error message:

Exception in thread "main" java.lang.IllegalArgumentException: Cannot encode phred score: 253
at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:255)
at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:243)
at net.sf.samtools.SAMUtils.phredToFastq(SAMUtils.java:229)
at net.sf.samtools.SAMRecord.getBaseQualityString(SAMRecord.java:239)
at net.sf.samtools.SAMTextWriter.writeAlignment(SAMTextWriter.java:100)
at net.sf.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:178)
at net.sf.picard.sam.FastqToSam.doUnpaired(FastqToSam.java:133)
at net.sf.picard.sam.FastqToSam.doWork(FastqToSam.java:111)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at net.sf.picard.sam.FastqToSam.main(FastqToSam.java:106)


Can anyone help me with this?

Is this something to do with installing ant? or SAM-JDK? I can't really figure it out and am working on a Mac OS X with all the developer tools installed. Please help.

[droog_22]

Hi,

It seems that the problem might be due to some illegale or out of range phred scores as the error message says "Cannot encode phred score: 253". You might want to have a look here http://en.wikipedia.org/wiki/FASTQ_format and check your FASTQ file if there are some strange quality score outliers or recheck the QUALITY_FORMAT option of FastqToSam.

Cheers, D.