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Description
If one of the input FASTQ files has a missing/blank sequence, the output FASTQ will be malformed.
I.e. if the input FASTQ has a correct entry followed by a blank entry like this:
@A00545
ACGTGCTGAC
+
FFF,:,FFFF
@A00546
+
where the sequence line and quality line are both blank, then the output will have a malformed entry, like so, where there is only a "+" and a quality sequence, but no read ID or genetic sequence:
@A00545
ACGTGCTGAC
+
FFF,:,FFFF
+
F:FFFFFFFF
The program should either throw an error if the FASTQ file has a blank entry, or skip the entry entirely in the output.
(In this case, I didn't know my FASTQ file had a blank entry—it came off the sequencer like that—but Fastp ran with no errors and I only discovered the problem during downstream analysis because the output FASTQ file was not correctly formed.)