summary.qual cannot handle "new" illumina data with max qual 41

[rrohwer]

The summary.qual command returns this error:

mothur > summary.qual(qfile=ERR1547032_1.qual)

Using 1 processors.
[ERROR]: ERR1547032.1 has a quality scores of 41, expecting values to be less than 40.

For a qual file looking like this:

mothur > system(head ERR1547032_1.qual)
>ERR1547032.1	34.06
31 34 34 37 35 35 37 37 37 37 39 39 39 41 38 39 38 37 38 40 38 38 40 41 41 40 40 41 41 36 38 38 39 40 41 40 38 30 37 39 40 37 39 41 40 40 40 40 31 34 32 35 35 35 35 35 28 33 35 35 35 31 34 29 26 32 31 34 35 35 35 34 34 31 31 25 10 25 25 19 29 29 33 24 29 33 32 34 32 34 25 34 34 34 35 27 13 10 25 31

Generated from a fastq file looking like this:

mothur > system(head -ER1547032_1.fastq)
@ERR1547032.1 1242.ME01Aug02EB1R1_0 length=100
TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACCCGAGCTCAACTTGGGTGCTG
+ERR1547032.1 1242.ME01Aug02EB1R1_0 length=100
@CCFDDFFFFHHHJGHGFGIGGIJJIIJJEGGHIJIG?FHIFHJIIII@CADDDDD=BDDD@C>;A@CDDDCC@@:+::4>>B9>BACAC:CCCD<.+:@

According to wikipedia (all I could find: https://en.wikipedia.org/wiki/FASTQ_format#Encoding) Illumina 1.8 and higher allows for quality values up to 41, while the older illumina and Sanger only had a max value of 40. So I think this means that this mothur command needs to be updated?

Thanks for your help!
Robin

[mothur-westcott]

Thanks for bringing this to our attention. We will add the fix to our next release.