usearch fatal error

[Irene Adamo]

Hi everyone,

I am trying to do the quality filtering of the sequences using this small
script:

for fq in out_trimmed/*_trimmed_primers2.fastq
do
usearch9 -fastq_filter ${fq} -fastq_maxee 1 -fastq_minlen 200 -fastaout
"${fq%.fastq}.fa"
done

I am getting this errors:

usearch9 -fastq_filter out_trimmed/C7P1_trimmed_primers2.fastq -fastq_maxee 1
-fastq_minlen 200 -fastaout out_trimmed/C7P1_trimmed_primers2.fa

---Fatal error---

CharToIntQual('K') Phred score 42 out of range 0..41

usearch9 -fastq_filter out_trimmed/C7P2_trimmed_primers2.fastq -fastq_maxee 1
-fastq_minlen 200 -fastaout out_trimmed/C7P2_trimmed_primers2.fa

---Fatal error---

CharToIntQual('L') Phred score 43 out of range 0..41

usearch9 -fastq_filter out_trimmed/C7P3_trimmed_primers2.fastq -fastq_maxee 1
-fastq_minlen 200 -fastaout out_trimmed/C7P3_trimmed_primers2.fa

---Fatal error---

../fastqfilter.cpp(132) assert failed: Qual != 0

I have looked online and on the website to see if there was any explanation for
these errors but I could not find anything, could help in understanding what is
the source of the problem?

thanks for any help

[Colin Brislawn]

Hello Irene,

Because this error has to do with usearch9 and this bash script, you would probably have the best luck contacting the usearch developer, Robert Edgar (r...@drive5.com). He is very responsive by email and super helpful.

(This forum is focused on supporting qiime)

Colin