BWA aligner error: paired reads have different names

Question

[MAPK]

Hi All,

I was trying to run bwa with paired FASTQ and ran over this problem below. How do I fix this error? Thanks!

[mem_sam_pe] paired reads have different names: "HISEQ2000B:573:C6027ACXX:1:2314:18", "HISEQ2000B:573:C6027ACXX:1:2314:18428:92556"

Command exited with non-zero status 1
        Command being timed: "bwa mem -t 4 -R @RG\tID:C6027ACXX:1\tPL:illumina\tPU:HISEQ2000B:573:C6027ACXX:1\tLB:8008286227\tSM:26_BDU_BDU98201\tDS:26_BDU_BDU98201^8008286227 -M /tmp//Homo_sapiens_assembly38.fasta /tmp//26_BDU_BDU98201^8008286227.HISEQ2000B^573^C6027ACXX^1.r1.fq.gz /tmp//26_BDU_BDU98201^8008286227.HISEQ2000B^573^C6027ACXX^1.r2.fq.gz"

[ATpoint]

Did you preprocess the reads, like trimming? If so how? The error indicates that fastq files are out of sync, now it is about finding out why that is.

[MAPK]

I don't have much information on the trimming as I received the samples from sequencing center already trimmed/pre-processed. I ran the pipeline again and this time it worked without making any change which I think is very weid.