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marbl / Winnowmap

Long read / genome alignment software
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failed to parse the FASTA/FASTQ record #27

Open Gongjiao94 opened 2 years ago

Gongjiao94 commented 2 years ago

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 commented 2 years ago

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

cjain7 commented 2 years ago

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 commented 2 years ago

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.