# Kneaddata log file error

**URL:** <https://forum.biobakery.org/t/kneaddata-log-file-error/1295>\
**Category:** KneadData\
**Created:** [November 17, 2020, 12:48pm UTC](https://forum.biobakery.org/t/kneaddata-log-file-error/1295 "2020-11-17T12:48:23Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![auas](https://avatars.discourse-cdn.com/v4/letter/a/bbce88/32.png) [@auas](https://forum.biobakery.org/u/auas)\
**Post date:** [November 17, 2020, 12:48pm UTC](https://forum.biobakery.org/t/kneaddata-log-file-error/1295/1 "2020-11-17T12:48:23Z")

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Dear developers,

I found an error in kneaddata log file. it seems that it wrongly matches the reference database and the decontaminated file. Below is a demo of the issue:

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/1X/58ef099281cf8ac5f1eacd72d48aaaa6b0506599.png)

the database is marked as hg37dec\_v0.1 but from the file name (_SILVA\_128_fastq), rRNA database is used at this step. This minor error leads to the merged log file wrongly report the number of reads get filtered at each step. It would be very helpful if you could help me to look into this issue.

Best wishes,  
Shen

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**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [June 3, 2021, 4:27pm UTC](https://forum.biobakery.org/t/kneaddata-log-file-error/1295/2 "2021-06-03T16:27:42Z")

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Hi @auas ,

Apologies for the late reply. Can you provide us the kneaddata command that you were using (reference database parameter)?

Regards,  
Sagun

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<div class="post-metadata">

**Author:** ![auas](https://avatars.discourse-cdn.com/v4/letter/a/bbce88/32.png) [@auas](https://forum.biobakery.org/u/auas)\
**Post date:** [June 15, 2021, 2:02pm UTC](https://forum.biobakery.org/t/kneaddata-log-file-error/1295/3 "2021-06-15T14:02:23Z")

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Hi Sagun,

Nice to hear from you. Below is the command I am using:

```auto
"kneaddata --reorder --serial --input {input.re_trimmed_p1} --input {input.re_trimmed_p2} -o {params.kneaddata_root} -db {params.rRNA} -db {params.hDNA} -db {params.hRNA} \
	 --run-fastqc-start --run-fastqc-end --remove-intermediate-output --trimmomatic-options 'HEADCROP:15 SLIDINGWINDOW:4:15 MINLEN:50' \
	 -t 4 --log {output.log_fp} --output-prefix {params.sample_id}"

```

And the reference databases are:

```auto
hg37_bt2="/data/TOOLS/kneaddata-0.7.10/reference_DB/hg37_bt2/hg37dec_v0.1"

```

```auto
hg38_mRNA_bt2="/data/TOOLS/kneaddata-0.7.10/reference_DB/hg38_mRNA_bt2/human_hg38_refMrna"

```

```auto
SILVA_128_rRNA_bt2="/data/TOOLS/kneaddata-0.7.10/reference_DB/SILVA_128_rRNA_bt2/SILVA_128_LSUParc_SSUParc_ribosomal_RNA"

```

Looking forward to hearing from you.  
Best wishes,  
Shen