Is it necessary to run trimmomatic before HUMAnN? My read number decreased from around 10000000 to 7000000 in forward read and 2000000 in reverse read

Microbial community profiling HUMAnN
3

Hi @lauren.j.mciver - I am using the kneaddata in paired-end reads for decontamination. And, it seems read number increased after the step. Here’s my command and output. PLease note the read counts in the output.
Command:
for R1 in *_1.fastq.gz ; do sampleName=${R1%%_1.fastq.gz}; kneaddata --input ${sampleName}_1.fastq.gz --input ${sampleName}_2.fastq.gz --reference-db /home/deepchandagcp/kneaddata_db/ --bypass-trim --threads 8 --cat-final-output --max-memory 20000m --output kneaddata_output/; done

Output:

Decompressing gzipped file …
Initial number of reads ( /data/Desktop/prjeb2054_test/kneaddata_output/decompressed_jgdduff0_ERR011093_Metagenomics_of_human_gut_metagenome_2.fastq ): 10856019.0
Initial number of reads ( /data/Desktop/prjeb2054_test/kneaddata_output/decompressed_lyqwh2a8_ERR011093_Metagenomics_of_human_gut_metagenome_1.fastq ): 10856019.0
Bypass trimming
Decontaminating …
Running bowtie2 …
Total reads after removing those found in reference database ( /data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneadd
ata_hg37dec_v0.1_bowtie2_paired_clean_1.fastq ): 19540240.0
Total reads after removing those found in reference database ( /data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneadd
ata_hg37dec_v0.1_bowtie2_paired_clean_2.fastq ): 2171138.0
Total reads after merging results from multiple databases ( /data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneaddata
_paired_1.fastq ): 19540240.0
Total reads after merging results from multiple databases ( /data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneaddata
_paired_2.fastq ): 2171138.0
Total reads after removing those found in reference database ( /data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneadd
ata_hg37dec_v0.1_bowtie2_unmatched_1_clean.fastq ): 594.0
Total reads after merging results from multiple databases ( /data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneaddata
_unmatched_1.fastq ): 594.0
Total reads after removing those found in reference database ( /data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneadd
ata_hg37dec_v0.1_bowtie2_unmatched_2_clean.fastq ): 0.0
Total reads after merging results from multiple databases ( /data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneaddata
_unmatched_2.fastq ): 0.0

Final output files created:
/data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneaddata_paired_1.fastq
/data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneaddata_paired_2.fastq
/data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneaddata_unmatched_1.fastq
/data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneaddata_unmatched_2.fastq
/data/Desktop/prjeb2054_test/kneaddata_output/ERR011093_Metagenomics_of_human_gut_metagenome_1_kneaddata.fastq

Why this is happening. I have gone through a previous post. But did not get any solution to it. Please help.

Thanks