Kneaddata error

[Lu Yang]

Hi, community,

I use the Kneaddata to filter the sequences.

Here is the code I use 
kneaddata --input ../18TB_C1_L003_1.fastq --input ../18TB_C1_L003_2.fastq --reference-db /home/silva_128 --output kneaddata_output_silva132 --run-bmtagger --threads 30

However, I got the error, see attachment. I have searched the website, no clues. Is there anyone who can help me with this?

Thanks in advance.

[Lauren McIver]

Hi - It looks like your input files might not be in fastq format. I would double check the format of your input files. It looks like they might possibly be output files from metaphlan2.

Thanks,

Lauren

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[Lu Yang]

Thanks. I see. Unexpected change of the raw file happended. 

在 2018年4月17日星期二 UTC-4下午1:58:28，Lauren McIver写道：

Hi - It looks like your input files might not be in fastq format. I would double check the format of your input files. It looks like they might possibly be output files from metaphlan2.

Thanks,

Lauren

On Mon, Apr 16, 2018 at 8:33 PM, Lu Yang <luyan...@gmail.com> wrote:

Hi, community,

I use the Kneaddata to filter the sequences.

Here is the code I use 
kneaddata --input ../18TB_C1_L003_1.fastq --input ../18TB_C1_L003_2.fastq --reference-db /home/silva_128 --output kneaddata_output_silva132 --run-bmtagger --threads 30

However, I got the error, see attachment. I have searched the website, no clues. Is there anyone who can help me with this?

Thanks in advance.

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[Lu Yang]

Hi, 

 

May I follow up a question? I attached my result files from kneaddata. Since I use the protocal listed in biobakery, no one seems make sense to me with the demo run result.

 

Since there are so many files produced as listed in the attachment file.txt. I am not sure which one was the filtered data taht can be used as the HUMAnN2 inputs. Based on the log file listed, I think the tailed 4 lines in the log file was the final files in this procedures. Just want make sure that they are the right files  for my next HUMAnN2 input. Is that correct?

 

Millions of thanks.

[Lauren McIver]

Hi - Yes, you are correct the final output files listed in the kneaddata log are the filtered reads that are used as input to humann2. You can just concatenate these files into a single file per sample. Alternatively, when running kneaddata you can add the option "--cat-final-output" which will generate a single output file for use with humann2.

Thanks,

Lauren

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[Lu Yang]

That makes more sense! Thank so much.

在 2018年4月17日星期二 UTC-4下午6:16:43，Lauren McIver写道：

Hi - Yes, you are correct the final output files listed in the kneaddata log are the filtered reads that are used as input to humann2. You can just concatenate these files into a single file per sample. Alternatively, when running kneaddata you can add the option "--cat-final-output" which will generate a single output file for use with humann2.

Thanks,

Lauren

On Tue, Apr 17, 2018 at 3:21 PM, Lu Yang <luyan...@gmail.com> wrote:

Hi, 

 

May I follow up a question? I attached my result files from kneaddata. Since I use the protocal listed in biobakery, no one seems make sense to me with the demo run result.

 

Since there are so many files produced as listed in the attachment file.txt. I am not sure which one was the filtered data taht can be used as the HUMAnN2 inputs. Based on the log file listed, I think the tailed 4 lines in the log file was the final files in this procedures. Just want make sure that they are the right files  for my next HUMAnN2 input. Is that correct?

 

Millions of thanks.

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