issue with kneaddata

Question

[noorehuma]

Hi, Im running kneaddata and getting the follwoing error. Also the script doesn't fail, it completes its job in 12 hour, I get the decontaminated bowtie2 output but with an error. The error is: "Error, fewer reads in file specified with -2 than in file specified with -1"

After ignoring the error, I went ahead and ran kraken2 and bracken. My samples are from pig but my final output has contamination from homo_sapiens present in the taxonomy file. I also know that pigs have somewhat similar genome to homo_sapiens. I than ran kneaddata with multiple contamination db (pis and homo_sapiens) but still getting homo_sapien contamination in final output. I don't know why my taxonomy abundance file has contamination. I was thinking maybe its because of the error im getting above. Can someone please guide. Thanks

Answer 1

[GenoMax]

"Error, fewer reads in file specified with -2 than in file specified with -1"

That is not good. What it means is that the two paired-end data files are out of sync. So the alignments you are getting are likely discordant/non-sense. If you had scanned/trimmed the data files independently then go back to the original data and re-do the trimming using both files together.

You could also use repair.sh from BBMap suite to bring your trimmed data files back in sync removing singleton reads.

After ignoring the error

See above.