seqtk produces different number of reads for paired end files

[Ruy Jauregui]

Hello!
I run these commands:
seqtk sample -s100 cJ288_1.fq 90000 > ./subsample/cJ288_1.fq
seqtk sample -s100 cJ288_2.fq 90000 > ./subsample/cJ288_2.fq

When I count the reads in the output I get:
cJ288_1.fq:89995
cJ288_2.fq:89998

What's going on?

[Heng Li]

Probably the input fastq are not paired.