The bioBakery help forum

Kneaddata empty outputs and nonstop run

Hi,
I’m trying to run Kneaddata with some pair-end NovaSeq data. I don’t know why I keep getting empty files as outputs. Also, the run will never stop. I’m wondering if there is any issues in my loop. Here is the loop I’m using and attached is the log file.

#group samples
files_knead_R1=ls | grep "R1_new.fastq"

#loop

for SAMPLE_READ1 in $files_knead_R1;

do
SAMPLE_OUT=echo $SAMPLE_READ1 | cut -d R -f1SAMPLE_OUT.fastq
SAMPLE_READ2=echo $SAMPLE_READ1 | cut -d R -f1R2_new.fastq
kneaddata -t 24 --input $SAMPLE_READ1 --input $SAMPLE_READ2 -db /blue/lorca/m.torrezlamberti/NS2074/RAW2/human_genome --output kneaddata_clean/$SAMPLE_OUTlog file.txt (4.1 KB)

done

On the other hand, I also tried the following codes
sed '1~4 s///1/g’ < original_R1.fastq > new_R1.fastq
sed '1~4 s///2/g’ < original_R2.fastq > new_R2.fastq

because I thought the issue could be that the R1 and R2 were not able to link. However that did not fix the issue above.

I’ll appreciate any help