Mismatched reads

Infrastructure and utilities KneadData
1

Hi,

Im using kneaddata on paired reads and I get the following error.

bowtie2: Error, fewer reads in file specified with -1 than in file specified with -2.

My script is:
#running kneaddata on PE reads

for i in R1_001.fastq.gz
do
filename=$(basename “$i”)
fname="${filename%_R_001.fastq.gz}"

kneaddata --decontaminate-pairs lenient --input1 ${fname}_R1_001.fastq.gz --input2 ${fname}_R2_001.fastq.gz --output kneaddata_out --reference-db /home/gomeza/huma0011/shotgun_pr/Sus_scrofa/Ensembl/Sscrofa11.1/Sequence/Bowtie2Index --remove-intermediate-output -t 5 -p 2 --trimmomatic-options “SLIDINGWINDOW:4:20 MINLEN:90”

Any idea what is going on?

2

Hi,
Can you double check that the files you are inputting are correct? Try explicitly putting the file names in the kneaddata command instead of using bash?
From the kneaddata end, I don’t see anything obviously wrong. Can you try removing the “–decontaminate-pairs lenient” option? We don’t recommend it, and it’s mainly there as legacy code.

Thanks,
Tom