# Kneaddata empty outputs and nonstop run

**URL:** https://forum.biobakery.org/t/kneaddata-empty-outputs-and-nonstop-run/1447
**Category:** KneadData
**Created:** [December 16, 2020, 9:16pm UTC](https://forum.biobakery.org/t/kneaddata-empty-outputs-and-nonstop-run/1447 "2020-12-16T21:16:45Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![MFTL](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mftl/32/2195_2.png) [@MFTL](https://forum.biobakery.org/u/MFTL)
#### Post date: [December 16, 2020, 9:16pm UTC](https://forum.biobakery.org/t/kneaddata-empty-outputs-and-nonstop-run/1447/1 "2020-12-16T21:16:45Z")

</div>

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 -f1`SAMPLE\_OUT.fastq  
SAMPLE\_READ2=`echo $SAMPLE_READ1 | cut -d R -f1`R2\_new.fastq  
kneaddata -t 24 --input $SAMPLE\_READ1 --input $SAMPLE\_READ2 -db /blue/lorca/m.torrezlamberti/NS2074/RAW2/human\_genome --output kneaddata\_clean/$SAMPLE\_OUT[log file.txt](https://forum.biobakery.org/uploads/short-url/fWF5ROfERHRlwc56t3wbpQBCSNK.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