Error in using USEARCH - Bad line 5 in FASTQ file 'sample_R1.fastq': expected '@'

Hello, everyone. I'm running the 32-bit USEARCH to do the paired-reads merging and yet I'm having a pizzle which I don't know how to resolve. When using the command "fastq_mergepairs", I faithfully follow the guide posted on drive5.com.

However, I got an error message saying "Bad line 5 in FASTQ file 'sample1_R1.fastq' : expected '@'.

I've checked the input fastq file, and I am sure it's contained 4 lines with the first line the label line starting with @. So, I didn't see what the line 5 means here. ..And how do I do the trouble shooting? Thanks for your help!

input usearch fastq fastqfile

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updated 5.2 years ago by Mensur Dlakic

• written 5.2 years ago by Yu •

I don't think that was your command line as listed, because you don't have sample1_R1.fastq in it.

What is the output of this command:

head sample1_R1.fastq

There are bunch of programs that can merge the reads, such as reformat.sh from BBTools.

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written 5.2 years ago by Mensur Dlakic

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