failed to parse the FASTA/FASTQ record

[Gongjiao94]

Dear @cjain7 ,
When I mapped the ONT reads to GRCh38 without alt sequence using winnowmap with version 2.0.3, it occured the warning message just like "failed to parse the FASTA/FASTQ record next to '783361e5-baa7-44de-9c84-4d1399aa5ceb". So what does this warning mean? Does it affect the final sam file. My command line shows as below:

winnowmap -W repetitive_k15.txt --cs --MD -L -t 32 -ax map-ont ${ref} ${fq} > out.sam

Thanks in advance
Jiao

[cjain7]

Can you also try minimap2 and see if the same warning is shown?

[cjain7]

Also, you may want to check the fastq file record to make sure it's properly formatted
One read is probably left unmapped in SAM file as per this warning.

[Gongjiao94]

Can you also try minimap2 and see if the same warning is shown?

Yes, I ran minimap2 with the same fastq file, and it showed the similar error "wrong FASTA/FASTQ record". Maybe some wrong goes to my fastq. I'll check it later. Thank you.