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OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
MIT License
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Error is raised for problematic rows #560

Open TomerAntman opened 6 months ago

TomerAntman commented 6 months ago

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 6 months ago

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 6 months ago

@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 5 months ago

Could you please upload a piece of your data so that I can reproduce this issue?     ------------------ Original ------------------ From: @.>; Date:  Sun, Jun 2, 2024 03:04 AM To: @.>; Cc: @.***>; Subject:  Re: [OpenGene/fastp] Error is raised for problematic rows (Issue #560)

 

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?

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