bwa-mem2 error: skip or orientatioon FF

Question

[jiyoung]

I am having some problems with using bwa-mem2 After using the command line(below): there is some error in my results. The error message stated: "Skip or orientation FR as there are not enough pairs. paired reads have different names.

How can I solve this problem?

below is my command line

base)/$ bwa mem -t 10 A.fasta virus_DKDN230027457-1A_HJHVHDSX7_L1.1qc.fq virus_DKDN230027457-1A_HJHVHDSX7_L1.2\ qc.fq > out.sam

Answer 1

[ATpoint]

The orientation is just an info, no warning/error. It's the name thing that is the problem. Have data been manipulated, like trimmed, and you used a trimmer not for paired-end data?

[jiyoung]

Thank u for your comment. In my case, i using the FASTP tool for trimming. Is this tool the problem? Would this be solved by using bowtie2 instead of bwa?

[ATpoint]

Did you process the paired-end data separately, so one run for R1 and one for R2? The message means that the R1 and R2 files are out-of-sync. YOu have to run both through fastp at the same time, see its manual on paired-end data. No, any aligner will choke on unsync data.

[jiyoung]

As you say, the problem was caused by the trim not being paired end. I've managed to fix this, thank you very much.