Need Help! Vsearch fastq_filter quality value above qmax

sciencepanda · 04-04-2019, 09:24 AM

Hello all!

I'm new to the community and just started my first bioinformatics project. I'm filtering out merged reads with the expected error of 1-100.

code I'm running:
vsearch -fastq_filter ./MergedFiles/${otp}_merged.fastq -fastq_maxee 1 -fastqout ./MergedFiles/${otp}_mergedfilt.fastq -fastaout ./MergedFiles/${otp}_mergedfilt.fasta

The issue is that when I run it, I get back a fatal error saying-

Reading input file 0%
Fatal error: FASTQ quality value (42) above qmax (41)

I've tried usearch, but my file is too big for the free 32-bit version, and I've tried replacing fastq_maxee 1 with fastq_qmax 42, but that doesn't filter anything out. I'm a bit new to all this and I'm stuck. Any help would be greatly appreciated!

-science panda

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04-04-2019, 09:24 AM	#1
sciencepanda Junior Member Location: orlando Join Date: Feb 2019 Posts: 1	Need Help! Vsearch fastq_filter quality value above qmax Hello all! I'm new to the community and just started my first bioinformatics project. I'm filtering out merged reads with the expected error of 1-100. code I'm running: vsearch -fastq_filter ./MergedFiles/${otp}_merged.fastq -fastq_maxee 1 -fastqout ./MergedFiles/${otp}_mergedfilt.fastq -fastaout ./MergedFiles/${otp}_mergedfilt.fasta The issue is that when I run it, I get back a fatal error saying- Reading input file 0% Fatal error: FASTQ quality value (42) above qmax (41) I've tried usearch, but my file is too big for the free 32-bit version, and I've tried replacing fastq_maxee 1 with fastq_qmax 42, but that doesn't filter anything out. I'm a bit new to all this and I'm stuck. Any help would be greatly appreciated! -science panda