Picard Error: IllegalArgumentException: Invalid fastq character:

sehrrot · 02-22-2012, 08:19 PM

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)

Quote:

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 · 02-22-2012, 09:15 PM

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

maubp · 02-22-2012, 11:57 PM

What is the weird characters? Try using hexdump.

sehrrot · 02-23-2012, 05:07 PM

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 · 02-24-2012, 12:30 AM

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

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02-22-2012, 09:15 PM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 766	Either the fastq was made wrongly, or the .sam was made wrongly. Those are not normal quality characters. Last edited by swbarnes2; 02-22-2012 at 09:18 PM.

02-22-2012, 11:57 PM	#3
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,171	What is the weird characters? Try using hexdump.

02-23-2012, 05:07 PM	#4
sehrrot Member Location: Australia Join Date: Jul 2010 Posts: 54	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")

02-24-2012, 12:30 AM	#5
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,171	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