Running paired-end metagenome, only 3 result files were generated

Microbial community profiling HUMAnN
1

Hi,

I’m running paired-end metagenome sequencing files in Humann3.9.

My first question is:
I have only three results - which are genefamilies.tsv, pathabundance.tsv and pathcoverage.tsv.
I know there should be 2 more output files from 1 file.

Why I don’t get the other two results?

And my second question is:
in case of using paired-end sequencing data, how can I merge those files (R1.fastq / R2.fastq) and interpret the results?
In previous questions in this forum - people suggested that there’s no point of concatenating reads before running Humann.
In this case, can I merge the results like this?

$ humann_join_tables --input humann_output/ --output humann_merged.tsv --file_name pathway_abundance

Thanks.

P.S.
FYI, Here’s a part of my script for running:

tail -n +2 “$SAMPLESHEET” | awk -F’\t’ ‘{print $2}’ | while read -r SAMPLE_NAME; do
SAMPLE_PATH=“$INPUT_DIR/$SAMPLE_NAME”
echo “Processing: $SAMPLE_NAME”

humann --input "$SAMPLE_PATH" --output "$OUTPUT_DIR"

if [ $? -eq 0 ]; then
    echo "Completed: $SAMPLE_NAME"
else
    echo "Failed: $SAMPLE_NAME"
fi

done

2

In HUMAnN 3.9 you only expect those 3 main output files per sample (plus some other stuff under sample temp). We have revised that in HUMAnN 4 to move more of the important files out of temp and to replace coverage with a new, more useful file (reaction abundance). Maybe you’re thinking of these v4 changes?

We recommend concatenating R1 and R2 before input to HUMAnN, equivalent to cat R1.fastq R2.fastq > NEW.fastq.

The word “merge” is sometimes used to mean overlapping paired R1 and R2 from the same sequencing fragment. That is not necessary or expected for HUMAnN (it’s more common in amplicon studies where you have done sequencing in which R1 and R2 actually overlap, and the merging helps to improve lower-quality bases at the ends of each reach, as well as create a longer sequence for clustering).