ERROR [mem_sam_pe] paired reads have different names -- during binning in metaWRAP pipeline
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11 weeks ago
arshad1292 ▴ 40

I performed the following steps with my data.

  1. Performed digital normalization on the individual 205 samples --- success
  2. removed the host (e.g. human) and adapter sequences from the individual samples --- success
  3. concatenated the samples into groups ---success
  4. performed the assembly with metaspades and megahit --- success
  5. Tried to perform binning step but it gives the following error:

    ERROR [mem_sam_pe] paired reads have different names: "A00534:36:HCHN3DRXX:2:1101:7437:1031", "A00534:36:HCHN3DRXX:2:1101:13693:1031"

Any idea how to fix this issue? Could it be digital normalization messing up the read names?

Would really appreciate your help!

metawrap • 287 views
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Do you understand what the problem is? Have you figured out which step introduced it?

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It could be digital normalization step because the reads without digital normalization work just fine. And within digital normalization, I needed to interleave the read1 and read2 into one. I did that with bbmap

reformat.sh in1=read1.fastq in2=read2.fastq

After performing digital normalizatin steps, I needed to convert interleaved reads back into read1 and read2. Again, I did that with bbmap as below:

reformat.sh in=interleaved.fq out1=read1.fastq out2=read2.fastq

However, when I run the qc step (for adaptor and host sequences removal), it gives the following error:

Error: bad read id in file A_case_diginorm/trimmed_2.fastq: expected A00534:36:HCHN3DRXX:2:1101:12644:1000, got A00534:36:HCHN3DRXX:2:1101:14705:1000

May be bbmap is not splitting the read1 and read2 properly and giving them proper name? Not sure.. Again, this error doesn't appear if I perform this step without digital normalization.

But is there any other tools that I can use to interleave and then later split the reads?

I would really appreciate the help

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maybe a couple of solutions can be found here: link

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Ok i have fixed the problem. I should not have used bbmap but should have used provided script with khmer.

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