What happen if no human reads were filtered at all?

[Ming Liao]

Hello, 

I used the for loop to run kneaddata for each sample. But there is one sample whose results are very different:

The sample WGC066624 got only two outputs: WGC066624D.fastq, and  WGC066624D_kneaddata.log

as you can see in WGC066624D_kneaddata.log

For comparison, I attached the log file of another sample's output, which is quite "normal".

this sample WGC066623D got four outputs: 

WGC066623D_kneaddata.fastq.gz 

WGC066623D_kneaddata.trimmed.fastq.gz

WGC066623D_kneaddata_Homo_sapiens_bowtie2_contam.fastq

WGC066623D_kneaddata.log

I am wondering whether the WGC066624 did not contain any human reads at all. Can anyone help to explain a little bit? Thanks

Best,

Ming

[Lauren McIver]

Hi Ming,

Thank you for attaching the log files. It looks like the run for WGC066624D ended when it was trying to decompress the gzipped input file. Do you know if there might be an issue with the compression of this file? My suggestion would be to try to decompress this file to see if there are any errors. If not, then try running the decompressed file through kneaddata. I believe this should resolve the error you are seeing.

Thank you,

Lauren

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