Empty paired files

Infrastructure and utilities KneadData
1

Hi there,

I have followed the tutorials with test data and all worked well. I am currently running kneaddata on metagenome files, but end up with empty paired files as per below. I’ve updated bowtie2 to 2.5.4 and still get the same result. Has this something to do with fastq headers? mine start with:

@A00151:309:GW210329000:3:1101:1669:1000 1:N:0:AGTGTGGA+ATGCTCCG

whereas the tutorial fastq star with:

@SRR3586068.94937

Any help would be greatly appreciated.

Command run:
kneaddata -i1 02_R1_001.fastq -i2 02_R2_001.fastq -o kneaddata_out -db /scratch/db_human_phix/ --trimmomatic /home/.local/bin/ -t 4 --trimmomatic-options “SLIDINGWINDOW:4:20 MINLEN:50” --bowtie2-options “–very-sensitive --dovetail” --bypass-trf

12G Jun 6 12:26 02_R1_001_kneaddata.trimmed.1.fastq
238M Jun 6 12:26 02_R1_001_kneaddata.trimmed.single.1.fastq
11G Jun 6 12:26 02_R1_001_kneaddata.trimmed.2.fastq
134M Jun 6 12:26 02_R1_001_kneaddata.trimmed.single.2.fastq
0 Jun 6 13:05 02_R1_001_kneaddata_GRCh38_PhiX_bowtie2_paired_contam_1.fastq
0 Jun 6 13:05 02_R1_001_kneaddata_GRCh38_PhiX_bowtie2_paired_contam_2.fastq
0 Jun 6 13:05 02_R1_001_kneaddata_paired_1.fastq
0 Jun 6 13:05 02_R1_001_kneaddata_paired_2.fastq
12G Jun 6 13:39 02_R1_001_kneaddata_unmatched_2.fastq
12G Jun 6 13:39 02_R1_001_kneaddata_unmatched_1.fastq
6M Jun 6 13:39 02_R1_001_kneaddata_GRCh38_PhiX_bowtie2_unmatched_2_contam.fastq
4.2M Jun 6 13:39 02_R1_001_kneaddata_GRCh38_PhiX_bowtie2_unmatched_1_contam.fastq
12K Jun 6 13:40 02_R1_001_kneaddata.log

2

I encountered the same problem. Have you managed to solve it?

3

It might help.

Alternatively, try installing the latest version, which is v0.12.1.

4

I installed the latest version v0.12.2 02-24-2025 and it is working fine.