Picard Error: IllegalArgumentException: Invalid fastq character:

[sehrrot]

hi all

I'm having trouble in using Picard to covert sam to bam. it seems to be halted by weird characters (I cannot type it here)

Ignoring SAM validation error due to lenient parsing:
Error parsing text SAM file. length(QUAL) != length(SEQ); Line 28
Line: DFCDZDN1:130:B01D5ACXX:4:1101:1099:2046 99 chr3 134076497 60 100M = 134076563 166 AGGGCAGAGGAGGGGAGAGAATGGCTCAGAGTCCTGAAGCACCACCTCCTTCAGATCAGTATCTCCACCATGTCTGACAAGTCCTGGANTCTGGATGTAG $$$''''%)))))++*+((**+*+++++**+'))++**++**+**+(*)++++))))()'''''''%&%%$$"$&%$$$$%"$%$%% (weird character here)
[Thu Feb 23 15:13:19 EST 2012] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=123666432
Exception in thread "main" java.lang.IllegalArgumentException: Invalid fastq character: (weird character here)
at net.sf.samtools.SAMUtils.fastqToPhred(SAMUtils.java:408)
at net.sf.samtools.SAMUtils.fastqToPhred(SAMUtils.java:387)
at net.sf.samtools.SAMRecord.setBaseQualityString(SAMRecord.java:254)
at net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:422)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:278)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:250)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:641)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:619)
at net.sf.picard.sam.SortSam.doWork(SortSam.java:67)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
at net.sf.picard.sam.SortSam.main(SortSam.java:79)

[swbarnes2]

Either the fastq was made wrongly, or the .sam was made wrongly. Those are not normal quality characters.

[maubp]

What is the weird characters? Try using hexdump.

[sehrrot]

Hi all

now it's working fine after I removed "-I" from bwa alignment process ("bwa aln -t 4 -f input.sai -I hg19 input.fastq")

[maubp]

So you probably have Sanger style FASTQ, which is what the latest Illumina pipeline produces - but you told bwa it was the legacy Illumina specific FASTQ encoding.

See:

http://en.wikipedia.org/wiki/FASTQ_format

http://dx.doi.org/10.1093/nar/gkp1137