usearch fatal error

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Irene Adamo

Nov 7, 2017, 8:13:13 AM11/7/17
to Qiime 1 Forum
Hi everyone,
I am trying to do the quality filtering of the sequences using this small

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

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

Nov 7, 2017, 4:49:07 PM11/7/17
to Qiime 1 Forum
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 ( He is very responsive by email and super helpful.

(This forum is focused on supporting qiime)


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