Winnowmap failed to parse the FASTA/FASTQ record

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

Sep 07 '21 02:09 Gongjiao94

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

Sep 08 '21 05:09 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.

Sep 08 '21 05:09 cjain7

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.

Sep 08 '21 07:09 Gongjiao94