NGS tutorial - Mapping trimmed fastq Files

Hi, I am working through the NGS tutorial ( Manupulating NGS data with Galaxy ). When I use BWA-MEM on the original fastq sample files ( sample1-f.fq.gz, sample1-r.fq.gz, sample2-f.fq.gz, sample2-r.fq.gz) then it works and I get mapped BAM files as shown in the tutorial. However if I try to run BWA-MEM on the trimmed fastq files generated before by Trimmomatic then mapping does not work but I get the error message:

[W::bseq_read] the 1st file has fewer sequences.
[M::mem_pestat] analyzing insert size distribution for orientation FF…
[M::mem_pestat] (25, 50, 75) percentile: (564, 1429, 1574)
[M::mem_pestat] low and high boundaries for computing mean and

So why doesn’t it work? In the tutorial it is suggested that the workflow should be continued with trimmed files (however in the video showing mapping with BWA-MEM the original, non-trimmed fastq files are used).

Thanks, Andreas