fastq-multx not returning correct number of fastq files

[liisa...@hotmail.com]

Hi,
I am using fastq-multx with the -l flag in a bash script

fastq-multx -l $1 $2 $3 -o %.R2.fastq -o %.R1.fastq

where $1 is the barcodes.grp file
where $2 is the R2.fastq.gz file
where $3 is the R1.fastq.gz file

I am expecting 96 R2.fastq files and 96 R1.fastq files but sometimes when I run the script I get 63 or 84. There are no errors or warnings printed to the screen so I do not know why am not getting the expected 96 fastq files (as there are in my barcodes file).

Any insight would be greatly appreciated.

Thanks in advance,
Liisa