Error when Interleaving data

[howla1ke]

Please help, I am brand new to bioinformatics. I trimmed all of my files with Trimmomatic, after unzipping I used Khmer to interleave R1/R2 of a sample. I ended up with 17 interleaved files, this should have been the 18th. R1/R2 of one sample will not interleave and I got this error: ...

0 pairs
ERROR: This doesn't look like paired data! K00368:239:HJV3MBBXY:6:1101:1184:1367 1:N:0:GTTCCGAT+GCAGGATT K00368:239:HJV3MBBXY:5:1101:1529:1367 2:N:0:ATTCCAAT+GGAGAATT

I then tried to interleave the raw data to see if it was a trimming issue and received the exact same error code. Is there anything else that I can do for this? Has anyone had this happen before? Can anyone suggest the next step?

[ctb]

Hi @howla1ke,

K00368:239:HJV3MBBXY:6:1101:1184:1367 1:N:0:GTTCCGAT+GCAGGATT

and

K00368:239:HJV3MBBXY:5:1101:1529:1367

do indeed look like they are not matched. This sounds like a problem with your raw data files.

If you use head -4 on each of the two FASTQ files you should be able to confirm that the sequence names don't match properly. If that's true, at that point I'd suggest asking the people who did your sequencing to take a look at those two files specifically.