usearch80 with Fatal error “Bad FASTQ record”

[xzron...@gmail.com]

Hi,

A fatal error come out when i run the 16s data using usearch 80 in qiime. How can i deal with it? The command and error as the following:

usearch80 -fastq_filter NHsplitlibrariesfastq_2/seqs.fastq -fastq_maxee 0.5 -fastq_trunclen 240 -fastaout ./usearch_qf_results_80_2/reads.fa

---Fatal error---

Bad FASTQ record: 411 bases, 264 quals line 8131960 file NHsplitlibrariesfastq_2/seqs.fastq label H12_2032989

Many thanks,

ZR xie

[Antonio González Peña]

Hi ZR xie, 

It seems like you are running usearch80, which is not supported by QIIME, and you are running it directly via the command line. Have you contacted the authors of usearch80?

Anyway, from the error it seems like your read/qual H12_2032989 (record) have different sizes. My guess is that you demuxed your files and the parser didn't store all the qual info.

Good luck and hope this helps.