screen.seqs Error Message

While I was running screen.seqs, I got this error message: “Error in reading your fastafile, at position -1. Blank name.” What is the cause of this error message?

It seems like mothur is trying to read beyond the end of your fastafile. This could occur if we miscounted the number of sequences in your file. Before version 1.11.0, we counted the number of ‘>’ characters in the fastafile, but some users had more ‘>’ characters in the file than sequences due to ‘>’ being part of a sequence name, causing this error. In version 1.11.0 we changed how we counted the sequences.

I actually do have the latest version and I’m pretty sure my commands are right since I am adhering to the Costello stool analysis posted on the website. Is there any other reason why this might be happening? I will double check my groups file and see what might be going on.

Could you send your fasta file and logfile to

Thanks for sending your files. I was able to track down the problem. When mothur uses multiple processors, we divide the files into pieces and the different processors each complete a piece. We store the starting positions in the file for each process. The position for process 8 was too large to fit in the data type we used. This will be changed for version 1.12.0. Thanks for your help in tracking down the bug.