Question: BWA aligner error: paired reads have different names
gravatar for MAPK
8 weeks ago by
MAPK1.7k wrote:

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"
bwa • 147 views
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by MAPK1.7k

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.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by ATpoint46k

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.

ADD REPLYlink written 8 weeks ago by MAPK1.7k
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