Error in barcode dispatch after trimming

[cbligaard]

Hi,
I have been using skewer for demultiplexing with the command /home/projects/cu_10049/apps/skewer/skewer -b -z -t 10 -x primers_forward.fa -y primers_reverse.fa file_R1.fastq.gz fil_R2.fastqz -o file --quiet and I get the following output in the log file:

206344 read pairs processed; of these:
     0 ( 0.00%) short read pairs filtered out after trimming by size control
     0 ( 0.00%) empty read pairs filtered out after trimming by size control
206344 (100.00%) read pairs available; of these:
132384 (64.16%) assigned read pairs available after processing
 73960 (35.84%) unassigned read pairs available after processing

Barcode dispatch after trimming:
category        count   percentage:
A01          0    0.00%
A02          0    0.00%
A03          0    0.00%
A04          0    0.00%
A05          0    0.00%
A06          0    0.00%
A07          0    0.00%
A08          0    0.00%
A09          0    0.00%
A10          0    0.00%
A11          0    0.00%
A12          0    0.00%
A13          0    0.00%
A14          1    0.00%
A15          1    0.00%
A16          1    0.00%
B01        311    0.23%
B02        403    0.30%

However, when I look at the output there are sequences in the files for A02 and multiple of the other AXX's (but none in A01). On the other hand, I get no sequences for B01, but I do get 403 for B02. Can you help me resolve this issue?