OpenGene/fastp

Error is raised for problematic rows

TomerAntman opened this issue · 3 comments

TomerAntman commented

In some of the fastq files that I have, there are some problematic rows, such as this:

AAAAAEEEE...
@NB552437:11:HY5W2BGXG:1:11101:12897:1306 1:N:0:GAATTCGT+GTCAGTAC

+

@NB552437:11:HY5W2BGXG:1:11101:22688:1308 1:N:0:GAATTCGT+GTCAGTAC
CAGCGAGGG...
+
AAAAAEEEE...
@NB552437:11:HY5W2BGXG:1:11101:9713:1313 1:N:0:GAATTCGT+GTCAGTAC
TTTTCTTGA...

These problematic rows crash the code and the error is:

Expected '+', got
ERROR: '+' expected

I tried just deleting the empty rows but it still doesn't work.
Trimmomatic seems to be able to bypass this issue (it doesn't crash)

nickgladman commented

Hello. I am having the same problem, which seems to be identical to #534.
"Expected '+', got CCACAGTGAGCCGCCGATTTGTTCCATGCCTGCAC...

It seems like it causes the run to terminate at the problematic read rather than continuing. @TomerAntman are the quality threshold parameters you're using for trimmomatic the same for the fastp run?

TomerAntman commented

@nickgladman yes they are as far as I remember. I solved this the other day by running seqkit sana on the files and then seqkit pair and then run fastp on the paired "rescued" reads. It solved the issue for most of my files

sfchen commented