and splitting fastq file by sample


I am trying to use command to split my raw fastq file into separate fastq files. So I have about 96 samples in one fastq file and I want to get each sample into separate file. I am trying to run following command:, oligos=oligos.oligos, fasta=F, format=sanger, checkorient=T)

Otherwise the command seems to work, but most of my sequences end into scrap-files and only very few into sample specific files. I am using exactly the same oligos file as I used when I ran the following commands for the original fastq files without problems (i.e. much larger amount of sequences were accepted):

make.contigs(ffastq= Lib_S1_L001_R1_001.fastq, rfastq= Lib_S1_L001_R2_001.fastq, processors=16)
trim.seqs(fasta=Lib_S1_L001_R1_001.trim.contigs.fasta, oligos=oligos.oligos, maxambig=0, maxhomop=8, pdiffs=0, bdiffs=0, processors=16)

All help is appreciated!