Hi, I am experiencing a problem while running BWA mem on paired end fastq file downloaded from NCBI SRA. When I ran BWA-mem it gives an error like:
[mem_sam_pe] paired reads have different names: "SRR3239806.1.1", "SRR3239806.1.2"
Example Fastq file:
@SRR3239806.1.1 1 length=100 TTGTGTAGGGTGGGTAGGCTCCATGTTTCCCAGCAAAGCTGGAGACATACAGACTACCTGGTGTTACATTTATTTCAGTGCCTCCTGAGTGTCTCTAAAT +SRR3239806.1.1 1 length=100 B@CDDFEFFHFFFI@GHIJGIJJJIJIIJJJGGHHIIIJJJJHIIGEHGIJIIIEGIGGHI@A=AHHFDEFFFFFEDEEECCDDDDD3<@CCCDDAC@CC
@SRR3239806.1.2 1 length=100
@SRR3239806.2.1 2 length=100
@SRR3239806.2.2 2 length=100
(I've just pasted the headers for the sake of brevity.) Can anyone explain how can I fix this error?
Is it actually an error or just a warning? Did you download the fastq files or convert them with SRAtools?
Its an error. I downloaded fastq file directly. It was a single file.