I have loaded multiple Illumina fastq files onto a server and I’m utilizing mothur via command line. My end goal is to use the trim.seqs maxhomop command to remove poly-A runs in my data, which has been successful for a number of the files I’ve entered. However for a handful I enter the command:

mothur >

And get the following:

[ERROR]: Blank quality name.

Another error reads:

[ERROR]: Lengths do not match for sequence D8GSQ5P1:2:1102:5739:28694#0/1. Read 101 characters for fasta and 100 characters for quality scores.

I’m not sure what to do about blank quality names, but is there a way to change a parameter to allow for different lengths of characters in the fasta and quality scores?

Additionally, is there a way to set up batch run to run from multiple fastq at the same time?

Thanks for your help!

What version of mothur are you using? Could there be an issue with the file you are trying to process? If you want to send the fastq file to I can try to troubleshoot it for you.