If you have a single fastq file that has single reads inbetween paris then this script can help you separate the pairs in r1, r2 and single reads.

deinterleave_fastq_merge

cat ../Batch1.fastq | \
awk -v se=se.fastq -v r1=r1.fastq -v r2=r2.fastq '
BEGIN {l5=0}
{
if (l5 == 0) {
    l1=$0; getline
}
else {
    l1=l5
}
l2=$0; getline; l3=$0; getline; l4=$0;

if (l1 ~ " 1:") { 
    getline; l5=$0;
    if (l5 ~ " 2:") {
        getline; l6=$0; getline; l7=$0; getline; l8=$0;
        printf "%s\n%s\n%s\n%s\n", l1,l2,l3,l4 > r1;
        printf "%s\n%s\n%s\n%s\n", l5,l6,l7,l8 > r2; l5=0;
    } else {
        printf "%s\n%s\n%s\n%s\n", l1,l2,l3,l4 > se;
    }
} else {
    printf "%s\n%s\n%s\n%s\n", l1,l2,l3,l4 > se;
}
}'