Hi Mothur developers and users,

I just started using Mothur for the analysis of SSU rRNA gene sequences generated on the Illumina platform.

The command gives me the following error:

lengths do not match. read 150 characters for fasta and 69 characters for quality scores.

Sounds like there is a problem in reading out the quality information and I would appreciate any suggestions for solving that problem.


Could you send your logfile and fastq file to


The fastq is quite large - but I sent the first lines - maybe it gets clear from that already what the problem might be. How long does it normally take for a reply?

[quote="westcott"] Could you send your logfile and fastq file to ? [/quote]

The problem is occurring because the very last sequence in the file has an error. It looks like some of the quality information is missing. I will the sequence name to the error message output so in the future problems like this will be easier to spot.

Thanks a lot!!

Sarah/Pat, releated question: I used to generate fasta files from illumina reads. the sequence names in fasta file look something like this: >3VFXHS1:294:D17ETACXX:3:1101:17192:3058. This was apparently ok when running classify.seqs; but I attempted to run a UniFrac analysis pipeline with the same data and Unifrac.weighted crashed with the following message: -bash-3.2$ Name: 3VFXHS1 is not in your groupfile, and will be disregarded. The fact that the error message truncates the sequence name at the first “:” makes me think that “:” is not acceptable in sequence names. Is this so? I am sending the log file to mothur.bugs@gmail.

many thanks,


The problem is in the tree file. The ‘:’ character is a special character in a tree. It is used to indicate a branch length will follow.