Re: [Samtools-help] picard FastqToSam throws exception because the header has no slash

[Tim F. <tfe...@br...>]

It's expecting both of your reads to terminate in read number tokens like "/1" and "/2".  It expects this as an error check to ensure that you are actually pairing together reads that go together.  Don't the read names coming out of the Illumina files usually have this information?

I suspect it's reasonable to allow exact match read names in the two files if no suffixes are present.  What exactly do the first records in each file look like?

-t

On Jul 19, 2010, at 4:02 PM, Michael Muratet wrote:

> Greetings
> 
> When attempting to convert fastq files to bam format with FastqToSam I  
> get an error about a missing slash:
> 
> [mmuratet@node0026 ~]$ java -Xmx2g -jar picard/FastqToSam.jar  
> QUALITY_FORMAT=Illumina FASTQ=als_data/SL1979.r1.fastq FASTQ2=als_data/ 
> SL1979.r2.fastq OUTPUT=SL1979.bam SAMPLE_NAME=SL1979
> [Mon Jul 19 14:46:53 CDT 2010] net.sf.picard.sam.FastqToSam  
> FASTQ=als_data/SL1979.r1.fastq FASTQ2=als_data/SL1979.r2.fastq  
> QUALITY_FORMAT=Illumina OUTPUT=SL1979.bam SAMPLE_NAME=SL1979     
> READ_GROUP_NAME=A SORT_ORDER=queryname TMP_DIR=/tmp/mmuratet  
> VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT  
> COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000
> [Mon Jul 19 14:46:53 CDT 2010] net.sf.picard.sam.FastqToSam done.
> Runtime.totalMemory()=505413632
> Exception in thread "main" net.sf.picard.PicardException: Pair read  
> name 1 must have a slash: HWUSI-EAS614_1:1:100:10000:10803:0:1:1 at  
> line 9 in file /gpfs/gpfs1/home/mmuratet/als_data/SL1979.r1.fastq
> 	at net.sf.picard.sam.FastqToSam.getReadNameTokens(FastqToSam.java:239)
> 	at net.sf.picard.sam.FastqToSam.getBaseName(FastqToSam.java:216)
> 	at net.sf.picard.sam.FastqToSam.doPaired(FastqToSam.java:140)
> 	at net.sf.picard.sam.FastqToSam.doWork(FastqToSam.java:96)
> 	at  
> net 
> .sf 
> .picard 
> .cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
> 	at net.sf.picard.sam.FastqToSam.main(FastqToSam.java:91)
> 
> I am not aware of a requirement to have a slash in fastq format, is  
> there one? The headers are straight from the Illumina pipeline.
> 
> Thanks
> 
> Mike
> 
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmu...@hu...
> (256) 327-0473 (p)
> (256) 327-0966 (f)
> 
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
> 
> 
> 
> 
> 
> 
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