problem with novoalign RG option

[zhacker]

Hello everyone,

I am trying to use novoalign for 108 illumina .fastq paired-end files (54 pairs) and for that I wrote a perl script that pairs up the files and runs novaalign on each pair. the perl line that generates the novoalign call is:


$rgoption = '$\'@RG\tID:'.$file1.'\tPL:illumina\tPU:illumina\tLB:tumour\tSM:'.$temp.'\'';
@system_args = ("novoalign", "-d", $REF, "-F", "STDFQ", "-f", $file1, $file2, "-r", "Random", "-K", $temp, "-o", "SAM", $rgoption, $temp1, ">" , $temp2);


the actual call generated by running this line becomes:


novoalign -d /scratch/data/reference_genomes/human/human_g1k_v37.fasta -F STDFQ -f 0099758_1_1sanger.fastq 0099758_1_2sanger.fastq -r Random -K 0099758_1_1sanger -o SAM $'@RG\tID:0099758_1_1sanger.fastq\tPL:illumina\tPU:illumina\tLB:tumour\tSM:0099758_1_1sanger' 0099758_1_1sanger.fastqnovo.stats > 0099758_1_1sanger.fastqnovo.raw.sam


Giving me the following error:

Problem processing command line arguments: Expecting @RG record with -o SAM option. at '$'@RG\tID:0099758_1_1sanger.fastq\tPL:illumina\tPU:illumina\tLB:tumour\tSM:0099758_1_1sanger''

It's not liking my RG record...the problem is that if I don't include it in my command, it asks for it saying that required RG record for -o SAM

Do you have any idea what I am doing wrong? I would highly appreciate your input. Thank you in advance.

[zhacker]

I just noticed that I am missing > before my .stats file, it's still giving me the same error though......your help will save my brain from exploding, Thank YOu!!!!

[zee]

Hi Zhacker,

I think you should place your SAM RG header in double quotes `""` rather than single quotes. i.e.

novoalign -d /scratch/data/reference_genomes/human/human_g1k_v37.fasta \
-F STDFQ -f 0099758_1_1sanger.fastq 0099758_1_2sanger.fastq \
-r Random -K 0099758_1_1sanger \
 -o SAM $"@RG\tID:0099758_1_1sanger.fastq\tPL:illumina\tPU:illumina\tLB:tumour\tSM:0099758_1_1sanger" 
2> 0099758_1_1sanger.fastqnovo.stats > 0099758_1_1sanger.fastqnovo.raw.sam

[zhacker]

Thank you for the reply zee and sorry about not getting back earlier. After scratching my head for a while I discovered that the problem's not in the novoalign command itself but it's in my perl script. I am using perl's system() to call novoalign which shouldn't be done because system() can only be used when you're not returning anything - not the case for my command. Thank you very much!