Why so few taxonomy genereted by humann?

We try to reanalyze this dataset.ENA Browser
However, only get about 200 taxonomy at the end. It is too few, compared with our other human microbiome dataset.
Thank you for your attention. This is my code.
time parallel -j 2 --xapply ‘kneaddata -i {1} -i {2} --remove-intermediate-output -o kneaddata_out
-db /home/shared/bowtiedb/GRCh38_PhiX --trimmomatic /usr/local/prg/Trimmomatic-0.36/
-t 4 --trimmomatic-options “SLIDINGWINDOW:4:20 MINLEN:50”
–bowtie2-options “–very-sensitive --dovetail”’ ::: *1.fastq.gz ::: *2.fastq.gz

concat_paired_end.pl -p 4 --no_R_match -o cat_reads kneaddata_out/paired.fastq

parallel -j 12 ‘humann2 --threads 12 --input {} --output humann2_out/{/.}’ ::: cat_reads/*fastq
#merge species
/usr/local/prg/metaphlan2/utils/merge_metaphlan_tables.py /media/sf_exerfeng/*tsv > metaphlan2_merged.tsv
#merge path
humann2_join_tables --input /media/sf_exerfeng/ --file_name pathabundance --output humann2_pathabundance.tsv
humann2_renorm_table --input humann2_pathabundance.tsv --units relab --output humann2_pathabundance_relab.tsv
humann2_split_stratified_table --input humann2_pathabundance_relab.tsv --output ./